Solution structure of the N-terminal extracellular domain of the lymphocyte receptor CD5 (CD5 domain 1)
MGSSHHHHHH SSGLVPRGSH MRLSWYDPDF QARLTRSNSK CQGQLEVYLK DGWHMVCSQS WGRSSKQWED PSQASKVCQR LNCGDPLSLG PFLKTYTPQS SIICYGQLGS FSNCSHSRND MCHSLGLTCL E
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS41:SG | 1:CYS83:SG |
2 | disulfide | sing | 1:CYS57:SG | 1:CYS122:SG |
3 | disulfide | sing | 1:CYS78:SG | 1:CYS129:SG |
4 | disulfide | sing | 1:CYS104:SG | 1:CYS114:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 79.6 % (1188 of 1493) | 79.7 % (622 of 780) | 80.4 % (459 of 571) | 75.4 % (107 of 142) |
Backbone | 81.7 % (632 of 774) | 82.4 % (220 of 267) | 81.4 % (311 of 382) | 80.8 % (101 of 125) |
Sidechain | 78.1 % (655 of 839) | 78.4 % (402 of 513) | 79.9 % (247 of 309) | 35.3 % (6 of 17) |
Aromatic | 70.7 % (106 of 150) | 70.7 % (53 of 75) | 69.0 % (49 of 71) | 100.0 % (4 of 4) |
Methyl | 87.5 % (77 of 88) | 88.6 % (39 of 44) | 86.4 % (38 of 44) |
1. CD5d1
MGSSHHHHHH SSGLVPRGSH MRLSWYDPDF QARLTRSNSK CQGQLEVYLK DGWHMVCSQS WGRSSKQWED PSQASKVCQR LNCGDPLSLG PFLKTYTPQS SIICYGQLGS FSNCSHSRND MCHSLGLTCL ESolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CD5d1 | [U-15N] | 1 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | EDTA | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | CD5d1 | [U-13C; U-15N] | 1 mM | |
8 | EDTA | natural abundance | 1 mM | |
9 | sodium phosphate | natural abundance | 50 mM | |
10 | sodium chloride | natural abundance | 200 mM | |
11 | H2O | natural abundance | 90 % | |
12 | D2O | natural abundance | 10 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | CD5d1 | [U-13C; U-15N] | 1 mM | |
14 | EDTA | natural abundance | 1 mM | |
15 | sodium phosphate | natural abundance | 50 mM | |
16 | sodium chloride | natural abundance | 200 mM | |
17 | D2O | natural abundance | 100 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CD5d1 | [U-15N] | 1 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | EDTA | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CD5d1 | [U-15N] | 1 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | EDTA | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CD5d1 | [U-15N] | 1 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | EDTA | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | CD5d1 | [U-13C; U-15N] | 1 mM | |
8 | EDTA | natural abundance | 1 mM | |
9 | sodium phosphate | natural abundance | 50 mM | |
10 | sodium chloride | natural abundance | 200 mM | |
11 | H2O | natural abundance | 90 % | |
12 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | CD5d1 | [U-13C; U-15N] | 1 mM | |
8 | EDTA | natural abundance | 1 mM | |
9 | sodium phosphate | natural abundance | 50 mM | |
10 | sodium chloride | natural abundance | 200 mM | |
11 | H2O | natural abundance | 90 % | |
12 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | CD5d1 | [U-13C; U-15N] | 1 mM | |
8 | EDTA | natural abundance | 1 mM | |
9 | sodium phosphate | natural abundance | 50 mM | |
10 | sodium chloride | natural abundance | 200 mM | |
11 | H2O | natural abundance | 90 % | |
12 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | CD5d1 | [U-13C; U-15N] | 1 mM | |
8 | EDTA | natural abundance | 1 mM | |
9 | sodium phosphate | natural abundance | 50 mM | |
10 | sodium chloride | natural abundance | 200 mM | |
11 | H2O | natural abundance | 90 % | |
12 | D2O | natural abundance | 10 % |
Varian UnityPlus - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | CD5d1 | [U-13C; U-15N] | 1 mM | |
8 | EDTA | natural abundance | 1 mM | |
9 | sodium phosphate | natural abundance | 50 mM | |
10 | sodium chloride | natural abundance | 200 mM | |
11 | H2O | natural abundance | 90 % | |
12 | D2O | natural abundance | 10 % |
Varian UnityPlus - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | CD5d1 | [U-13C; U-15N] | 1 mM | |
8 | EDTA | natural abundance | 1 mM | |
9 | sodium phosphate | natural abundance | 50 mM | |
10 | sodium chloride | natural abundance | 200 mM | |
11 | H2O | natural abundance | 90 % | |
12 | D2O | natural abundance | 10 % |
Varian INOVA - 800 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | CD5d1 | [U-13C; U-15N] | 1 mM | |
14 | EDTA | natural abundance | 1 mM | |
15 | sodium phosphate | natural abundance | 50 mM | |
16 | sodium chloride | natural abundance | 200 mM | |
17 | D2O | natural abundance | 100 % |
Varian INOVA - 800 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | CD5d1 | [U-13C; U-15N] | 1 mM | |
14 | EDTA | natural abundance | 1 mM | |
15 | sodium phosphate | natural abundance | 50 mM | |
16 | sodium chloride | natural abundance | 200 mM | |
17 | D2O | natural abundance | 100 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15189_2jop.nef |
Input source #2: Coordindates | 2jop.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
Whether the assembly has a other bond | None |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
A:44:CYS:SG | A:86:CYS:SG | unknown | oxidized, CA 54.975, CB 44.929 ppm | 2.023 |
A:60:CYS:SG | A:125:CYS:SG | oxidized, CA 55.445, CB 38.263 ppm | oxidized, CA 55.246, CB 43.289 ppm | 2.026 |
A:81:CYS:SG | A:132:CYS:SG | oxidized, CA 57.795, CB 39.441 ppm | oxidized, CA 53.383, CB 42.627 ppm | 2.021 |
A:107:CYS:SG | A:117:CYS:SG | oxidized, CA 54.862, CB 46.483 ppm | oxidized, CA 55.576, CB 49.475 ppm | 2.015 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MGSSHHHHHHSSGLVPRGSHMRLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MGSSHHHHHHSSGLVPRGSHMRLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ----110-------120-------130---- SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE ||||||||||||||||||||||||||||||| SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE -------110-------120-------130-
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 131 | 0 | 0 | 100.0 |
Content subtype: combined_15189_2jop.nef
Assigned chemical shifts
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MGSSHHHHHHSSGLVPRGSHMRLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .....................RLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS ----110-------120-------130---- SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE ||||||||||||||||||||||||||||||| SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 780 | 610 | 78.2 |
13C chemical shifts | 571 | 453 | 79.3 |
15N chemical shifts | 149 | 105 | 70.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 267 | 216 | 80.9 |
13C chemical shifts | 262 | 207 | 79.0 |
15N chemical shifts | 125 | 101 | 80.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 513 | 394 | 76.8 |
13C chemical shifts | 309 | 246 | 79.6 |
15N chemical shifts | 24 | 4 | 16.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 48 | 41 | 85.4 |
13C chemical shifts | 48 | 41 | 85.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 75 | 52 | 69.3 |
13C chemical shifts | 71 | 48 | 67.6 |
15N chemical shifts | 4 | 4 | 100.0 |
Covalent bonds
Distance restraints
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MGSSHHHHHHSSGLVPRGSHMRLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS ||||||||||||||| || | |||||||| ||||||||| || |||||| ||||||||||| ||||| |||||| | ......................LSWYDPDFQARLTRS.SK.Q.QLEVYLKD.WHMVCSQSW.RS.KQWEDP.QASKVCQRLNC.DPLSL..FLKTYT.Q. ----110-------120-------130---- SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE ||||| || |||||| |||||| || ||||| SIICY.QL.SFSNCS.SRNDMC.SL.LTCLE
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MGSSHHHHHHSSGLVPRGSHMRLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS |||| | |||||| | |||||||| |||||||||| | ||||| || || |||||||||| || || .....................RLSW..P.FQARLT.S....QGQLEVYL...WHMVCSQSWG....Q...PSQAS.VC.RL.CGDPLSLGPF...YT.QS -----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- ----110-------120-------130---- SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE |||||| ||||| |||| |||||||| SIICYG.LGSFS.CSHS.....HSLGLTCL ----110-------120-------130---
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MGSSHHHHHHSSGLVPRGSHMRLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .....................RLSWYDPDFQARLTRSNSK.QGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS ----110-------120-------130---- SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE ||||||||||||||||||||||||||||||| SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE
Dihedral angle restraints
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MGSSHHHHHHSSGLVPRGSHMRLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRLNCGDPLSLGPFLKTYTPQS |||| ||||||| ||||||||| | |||| | | | |||||||||| ||||||| ||||||| | ......................LSWY..DFQARLT.....CQGQLEVYL.D..HMVC.....R....W.D..QASKVCQRLN.GDPLSLG.FLKTYTP.S ----110-------120-------130---- SIICYGQLGSFSNCSHSRNDMCHSLGLTCLE |||||||| |||||| | |||||| | SIICYGQL.....CSHSRN..C.SLGLTC.E