NMR Structure of the C-Terminal Domain of human APOBEC3B
MEILRYLMDP DTFTFNFNND PLVLRRRQTY LCYEVERLDN GTWVLMDQHM GFLCNEAKNL LCGFYGRHAE LRFLDLVPSL QLDPAQIYRV TWFISWSPCF SWGCAGEVRA FLQENTHVRL RIFAARIYDY DPLYKEALQM LRDAGAQVSI MTYDEFEYCW DTFVYRQGCP FQPWDGLEEH SQALSGRLRA ILQNQGNLEH HHHHH
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 71.1 % (1772 of 2493) | 78.3 % (1012 of 1293) | 57.1 % (557 of 976) | 90.6 % (203 of 224) |
Backbone | 80.4 % (976 of 1214) | 91.3 % (377 of 413) | 68.9 % (416 of 604) | 92.9 % (183 of 197) |
Sidechain | 65.9 % (970 of 1473) | 71.9 % (633 of 880) | 56.2 % (318 of 566) | 70.4 % (19 of 27) |
Aromatic | 38.5 % (127 of 330) | 69.7 % (115 of 165) | 3.8 % (6 of 159) | 100.0 % (6 of 6) |
Methyl | 91.7 % (187 of 204) | 96.1 % (98 of 102) | 87.3 % (89 of 102) |
1. A3B-CTD
MEILRYLMDP DTFTFNFNND PLVLRRRQTY LCYEVERLDN GTWVLMDQHM GFLCNEAKNL LCGFYGRHAE LRFLDLVPSL QLDPAQIYRV TWFISWSPCF SWGCAGEVRA FLQENTHVRL RIFAARIYDY DPLYKEALQM LRDAGAQVSI MTYDEFEYCW DTFVYRQGCP FQPWDGLEEH SQALSGRLRA ILQNQGNLEH HHHHHSolvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | A3B-CTD | [U-13C; U-15N; U-2H] | 0.08 mM | |
2 | Zinc | natural abundance | 0.08 mM | |
3 | D2O | [U-100% 2H] | 7 % | |
4 | H2O | natural abundance | 93 % | |
5 | DTT | natural abundance | 10 mM | |
6 | sodium phosphate | natural abundance | 25 mM |
Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | A3B-CTD | [U-100% 13C; U-100% 15N] | 0.08 mM | |
8 | Zinc | natural abundance | 0;08 mM | |
9 | D2O | [U-100% 2H] | 7 % | |
10 | H2O | natural abundance | 93 % | |
11 | DTT | natural abundance | 10 mM | |
12 | sodium phosphate | natural abundance | 25 mM |
Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | A3B-CTD | natural abundance | 0.05 mM | |
14 | Zinc | natural abundance | 0.05 mM | |
15 | D2O | [U-100% 2H] | 7 % | |
16 | H2O | natural abundance | 93 % | |
17 | DTT | natural abundance | 10 mM | |
18 | sodium phosphate | natural abundance | 25 mM |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 50.0 % (2491 of 4986) | 53.7 % (1388 of 2586) | 35.9 % (701 of 1952) | 89.7 % (402 of 448) |
Backbone | 59.8 % (1453 of 2428) | 71.1 % (587 of 826) | 42.0 % (507 of 1208) | 91.1 % (359 of 394) |
Sidechain | 41.8 % (1230 of 2946) | 45.0 % (792 of 1760) | 35.0 % (396 of 1132) | 77.8 % (42 of 54) |
Aromatic | 25.3 % (167 of 660) | 41.8 % (138 of 330) | 5.3 % (17 of 318) | 100.0 % (12 of 12) |
Methyl | 54.7 % (223 of 408) | 56.9 % (116 of 204) | 52.5 % (107 of 204) |
1. A3B-CTD
MEILRYLMDP DTFTFNFNND PLVLRRRQTY LCYEVERLDN GTWVLMDQHM GFLCNEAKNL LCGFYGRHAE LRFLDLVPSL QLDPAQIYRV TWFISWSPCF SWGCAGEVRA FLQENTHVRL RIFAARIYDY DPLYKEALQM LRDAGAQVSI MTYDEFEYCW DTFVYRQGCP FQPWDGLEEH SQALSGRLRA ILQNQGNLEH HHHHHSolvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | A3B-CTD | [U-100% 13C; U-100% 15N] | 0.08 mM | |
8 | Zinc | natural abundance | 0;08 mM | |
9 | D2O | [U-100% 2H] | 7 % | |
10 | H2O | natural abundance | 93 % | |
11 | DTT | natural abundance | 10 mM | |
12 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | A3B-CTD | [U-13C; U-15N; U-2H] | 0.08 mM | |
2 | Zinc | natural abundance | 0.08 mM | |
3 | D2O | [U-100% 2H] | 7 % | |
4 | H2O | natural abundance | 93 % | |
5 | DTT | natural abundance | 10 mM | |
6 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | A3B-CTD | [U-100% 13C; U-100% 15N] | 0.08 mM | |
8 | Zinc | natural abundance | 0;08 mM | |
9 | D2O | [U-100% 2H] | 7 % | |
10 | H2O | natural abundance | 93 % | |
11 | DTT | natural abundance | 10 mM | |
12 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | A3B-CTD | [U-13C; U-15N; U-2H] | 0.08 mM | |
2 | Zinc | natural abundance | 0.08 mM | |
3 | D2O | [U-100% 2H] | 7 % | |
4 | H2O | natural abundance | 93 % | |
5 | DTT | natural abundance | 10 mM | |
6 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | A3B-CTD | [U-13C; U-15N; U-2H] | 0.08 mM | |
2 | Zinc | natural abundance | 0.08 mM | |
3 | D2O | [U-100% 2H] | 7 % | |
4 | H2O | natural abundance | 93 % | |
5 | DTT | natural abundance | 10 mM | |
6 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | A3B-CTD | [U-100% 13C; U-100% 15N] | 0.08 mM | |
8 | Zinc | natural abundance | 0;08 mM | |
9 | D2O | [U-100% 2H] | 7 % | |
10 | H2O | natural abundance | 93 % | |
11 | DTT | natural abundance | 10 mM | |
12 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | A3B-CTD | [U-100% 13C; U-100% 15N] | 0.08 mM | |
8 | Zinc | natural abundance | 0;08 mM | |
9 | D2O | [U-100% 2H] | 7 % | |
10 | H2O | natural abundance | 93 % | |
11 | DTT | natural abundance | 10 mM | |
12 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | A3B-CTD | [U-13C; U-15N; U-2H] | 0.08 mM | |
2 | Zinc | natural abundance | 0.08 mM | |
3 | D2O | [U-100% 2H] | 7 % | |
4 | H2O | natural abundance | 93 % | |
5 | DTT | natural abundance | 10 mM | |
6 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | A3B-CTD | [U-13C; U-15N; U-2H] | 0.08 mM | |
2 | Zinc | natural abundance | 0.08 mM | |
3 | D2O | [U-100% 2H] | 7 % | |
4 | H2O | natural abundance | 93 % | |
5 | DTT | natural abundance | 10 mM | |
6 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | A3B-CTD | natural abundance | 0.05 mM | |
14 | Zinc | natural abundance | 0.05 mM | |
15 | D2O | [U-100% 2H] | 7 % | |
16 | H2O | natural abundance | 93 % | |
17 | DTT | natural abundance | 10 mM | |
18 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | A3B-CTD | [U-100% 13C; U-100% 15N] | 0.08 mM | |
8 | Zinc | natural abundance | 0;08 mM | |
9 | D2O | [U-100% 2H] | 7 % | |
10 | H2O | natural abundance | 93 % | |
11 | DTT | natural abundance | 10 mM | |
12 | sodium phosphate | natural abundance | 25 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | A3B-CTD | [U-100% 13C; U-100% 15N] | 0.08 mM | |
8 | Zinc | natural abundance | 0;08 mM | |
9 | D2O | [U-100% 2H] | 7 % | |
10 | H2O | natural abundance | 93 % | |
11 | DTT | natural abundance | 10 mM | |
12 | sodium phosphate | natural abundance | 25 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_25985_2nbq.nef |
Input source #2: Coordindates | 2nbq.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | None |
Whether the assembly has a other bond | True (see coodinates for details) |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Ã…) |
---|---|---|---|---|
1:104:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:99:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:68:HIS:ND1 | 2:1:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | ZN | ZINC ION | None |
Sequence alignments
--190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- MEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 --290-------300-------310-------320-------330-------340-------350-------360-------370-------380----- SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 --390 HHHHH ||||| HHHHH -----
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 205 | 0 | 0 | 100.0 |
Content subtype: combined_25985_2nbq.nef
Assigned chemical shifts
--190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- MEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF ||||||||||||||||||| || |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| MEILRYLMDPDTFTFNFNN.PL...RRQTYLCYEVERLDNGTWVLMDQHMGFL.NEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF --290-------300-------310-------320-------330-------340-------350-------360-------370-------380----- SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH --390 HHHHH |||| .HHHH
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 1293 | 960 | 74.2 |
13C chemical shifts | 976 | 481 | 49.3 |
15N chemical shifts | 240 | 199 | 82.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 413 | 368 | 89.1 |
13C chemical shifts | 410 | 187 | 45.6 |
15N chemical shifts | 197 | 180 | 91.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 880 | 592 | 67.3 |
13C chemical shifts | 566 | 294 | 51.9 |
15N chemical shifts | 43 | 19 | 44.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 108 | 100 | 92.6 |
13C chemical shifts | 108 | 91 | 84.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 165 | 111 | 67.3 |
13C chemical shifts | 159 | 0 | 0.0 |
15N chemical shifts | 6 | 6 | 100.0 |
--190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- MEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF |||||| |||| ||| || ||||||||||||||||| |||||| | | ||||||||||||||||| ||||| ||||||||||||| || ..ILRYLM..DTFT..FNN.......RQ.YLCYEVERLDNGTWVLM.QHMGFL..E.K..LCGFYGRHAELRFLDLV.SLQLD.AQIYRVTWFISWS.CF --290-------300-------310-------320-------330-------340-------350-------360-------370-------380----- SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH ||||||||||||||||||||||| || |||| |||||||| ||||||||||||||||||||||||| || || |||||| |||||||||||||||||||| SWGCAGEVRAFLQENTHVRLRIF.AR.YDYD.LYKEALQM.RDAGAQVSIMTYDEFEYCWDTFVYR.GC.FQ.WDGLEE.SQALSGRLRAILQNQGNLEH --390 HHHHH || ...HH
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 1293 | 199 | 15.4 |
15N chemical shifts | 240 | 189 | 78.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 413 | 169 | 40.9 |
15N chemical shifts | 197 | 170 | 86.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 880 | 30 | 3.4 |
15N chemical shifts | 43 | 19 | 44.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 108 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 165 | 6 | 3.6 |
15N chemical shifts | 6 | 6 | 100.0 |
Covalent bonds
Distance restraints
--190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- MEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF ||||||||||||||||||| | |||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||||| MEILRYLMDPDTFTFNFNN..L.....QTYLCYEVERLDNGTWVLMDQHMGFL.NEAKNLLCGFY.RHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF --190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- --290-------300-------310-------320-------330-------340-------350-------360-------370-------380----- SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SWGCAGEVRAFLQENTHVRLRIFAARIYDYD.LYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGN --290-------300-------310-------320-------330-------340-------350-------360-------370-------380-- --390 HHHHH
--190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- MEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF |||||||||| |||||||||| | | || ||| | |||||||||||||| ||||||||| ........DPDTFTFNFN...........YLCYEVERLD..T.V.MD.HMG.L..............HAELRFLDLVPSLQ.....IYRVTWFIS..... --190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- --290-------300-------310-------320-------330-------340-------350-------360-------370-------380----- SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH |||||||||||| | ||||||| ||||||||||| | | |||||||||||||| ||||||||||||||||| ...CAGEVRAFLQEN.H.RLRIFAA.......LYKEALQMLRD...Q.S.MTYDEFEYCWDTFV...........GLEEHSQALSGRLRAIL --290-------300-------310-------320-------330-------340-------350-------360-------370------- --390 HHHHH
Dihedral angle restraints
--190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- MEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF ||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| ......LMDPDTFTFNFNN.......RQTYLCYEVERLDNGTWVLMDQHMGFLCNEA.NLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCF --190-------200-------210-------220-------230-------240-------250-------260-------270-------280----- --290-------300-------310-------320-------330-------340-------350-------360-------370-------380----- SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGNLEH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQ --290-------300-------310-------320-------330-------340-------350-------360-------370-------- --390 HHHHH