Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS11:SG | 1:CYS36:SG |
2 | disulfide | sing | 1:CYS11:SG | 1:CYS36:SG |
3 | disulfide | sing | 1:CYS13:SG | 1:CYS52:SG |
4 | disulfide | sing | 1:CYS13:SG | 1:CYS52:SG |
5 | disulfide | sing | 1:CYS38:SG | 1:CYS67:SG |
6 | disulfide | sing | 1:CYS67:SG | 1:CYS38:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 87.3 % (1130 of 1294) | 88.6 % (606 of 684) | 85.1 % (418 of 491) | 89.1 % (106 of 119) |
Backbone | 90.5 % (583 of 644) | 90.4 % (197 of 218) | 89.8 % (289 of 322) | 93.3 % (97 of 104) |
Sidechain | 85.1 % (642 of 754) | 87.8 % (409 of 466) | 82.1 % (224 of 273) | 60.0 % (9 of 15) |
Aromatic | 73.9 % (68 of 92) | 91.3 % (42 of 46) | 55.6 % (25 of 45) | 100.0 % (1 of 1) |
Methyl | 91.1 % (82 of 90) | 93.3 % (42 of 45) | 88.9 % (40 of 45) |
1. CXCL12/SDF1-alpha
GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCACQI VARLKNNNRQ VCIDPKLKWI QEYLEKCLNK2. CXCR4
GSMEGISIYT SDNYTEEMGS GDXDSMKEPA FREENANFNKSolvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.338 mM CXCL12 U-15N/13C (dimer concentration), 0.970 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 0.338 mM | |
2 | CXCR4 | natural abundance | 0.970 mM | |
3 | MES(d13) | 25 mM | ||
4 | H2O | 90 % | ||
5 | D2O | 10 % |
Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 1.07 mM CXCR4 U-15N/13C, 0.670 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.07 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.67 mM | |
8 | MES(d13) | 25 mM | ||
9 | H2O | 90 % | ||
10 | D2O | 10 % |
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 | internal | 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 | internal | 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 | internal | 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 | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.338 mM CXCL12 U-15N/13C (dimer concentration), 0.970 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 0.338 mM | |
2 | CXCR4 | natural abundance | 0.970 mM | |
3 | MES(d13) | 25 mM | ||
4 | H2O | 90 % | ||
5 | D2O | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.338 mM CXCL12 U-15N/13C (dimer concentration), 0.970 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 0.338 mM | |
2 | CXCR4 | natural abundance | 0.970 mM | |
3 | MES(d13) | 25 mM | ||
4 | H2O | 90 % | ||
5 | D2O | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.338 mM CXCL12 U-15N/13C (dimer concentration), 0.970 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 0.338 mM | |
2 | CXCR4 | natural abundance | 0.970 mM | |
3 | MES(d13) | 25 mM | ||
4 | H2O | 90 % | ||
5 | D2O | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.338 mM CXCL12 U-15N/13C (dimer concentration), 0.970 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 0.338 mM | |
2 | CXCR4 | natural abundance | 0.970 mM | |
3 | MES(d13) | 25 mM | ||
4 | H2O | 90 % | ||
5 | D2O | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 1.07 mM CXCR4 U-15N/13C, 0.670 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.07 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.67 mM | |
8 | MES(d13) | 25 mM | ||
9 | H2O | 90 % | ||
10 | D2O | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 1.07 mM CXCR4 U-15N/13C, 0.670 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.07 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.67 mM | |
8 | MES(d13) | 25 mM | ||
9 | H2O | 90 % | ||
10 | D2O | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 1.07 mM CXCR4 U-15N/13C, 0.670 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.07 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.67 mM | |
8 | MES(d13) | 25 mM | ||
9 | H2O | 90 % | ||
10 | D2O | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 1.07 mM CXCR4 U-15N/13C, 0.670 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.07 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.67 mM | |
8 | MES(d13) | 25 mM | ||
9 | H2O | 90 % | ||
10 | D2O | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15635_2k03.nef |
Input source #2: Coordindates | 2k03.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 | True (see coodinates for details) |
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 (Ã…) |
---|---|---|---|---|
A:9:CYS:SG | A:34:CYS:SG | oxidized, CA 53.192, CB 40.897 ppm | oxidized, CA 55.447, CB 45.228 ppm | 2.018 |
A:11:CYS:SG | A:50:CYS:SG | unknown | oxidized, CA 58.054, CB 43.375 ppm | 2.015 |
A:36:CYS:SG | C:265:CYS:SG | oxidized, CA 58.616, CB 45.705 ppm | unknown | 2.024 |
A:65:CYS:SG | C:236:CYS:SG | oxidized, CA 56.329, CB 45.235 ppm | unknown | 2.019 |
C:209:CYS:SG | C:234:CYS:SG | unknown | unknown | 2.032 |
C:211:CYS:SG | C:250:CYS:SG | unknown | unknown | 2.032 |
Other 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…) |
---|---|---|---|---|
3:22:ASP:C | 3:23:TYS:N | unknown | unknown | n/a |
3:23:TYS:C | 3:24:ASP:N | unknown | unknown | n/a |
4:22:ASP:C | 4:23:TYS:N | unknown | unknown | n/a |
4:23:TYS:C | 4:24:ASP:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 121 | TYS | O-SULFO-L-TYROSINE | Assigned chemical shifts, Distance restraints, Coordinates |
D | 321 | TYS | O-SULFO-L-TYROSINE | Distance restraints, Coordinates |
Sequence alignments
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK --------10--------20--------30--------40--------50--------60--------70
-100-----110-------120-------130-------- GSMEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK |||||||||||||||||||||||||||||||||||||||| GSMEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK --------10--------20--------30--------40
-200-----210-------220-------230-------240-------250-------260-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK --------10--------20--------30--------40--------50--------60--------70
-300-----310-------320-------330-------- GSMEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK |||||||||||||||||||||||||||||||||||||||| GSMEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK --------10--------20--------30--------40
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 70 | 0 | 0 | 100.0 |
B | B | 40 | 0 | 0 | 100.0 |
C | C | 70 | 0 | 0 | 100.0 |
D | D | 40 | 0 | 0 | 100.0 |
Content subtype: combined_15635_2k03.nef
Assigned chemical shifts
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ..KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLK..NRQVCIDPKLKWIQEYLEKCLNK
-100-----110-------120-------130-------- GSMEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK |||||||||||||||||||||||||||||||||||||| ..MEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 461 | 416 | 90.2 |
15N chemical shifts | 82 | 70 | 85.4 |
13C chemical shifts | 330 | 285 | 86.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 137 | 125 | 91.2 |
15N chemical shifts | 66 | 61 | 92.4 |
13C chemical shifts | 140 | 122 | 87.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 324 | 291 | 89.8 |
15N chemical shifts | 16 | 9 | 56.2 |
13C chemical shifts | 190 | 163 | 85.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 38 | 36 | 94.7 |
13C chemical shifts | 38 | 34 | 89.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 28 | 26 | 92.9 |
15N chemical shifts | 1 | 1 | 100.0 |
13C chemical shifts | 27 | 17 | 63.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 231 | 204 | 88.3 |
15N chemical shifts | 44 | 36 | 81.8 |
13C chemical shifts | 166 | 140 | 84.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 83 | 76 | 91.6 |
15N chemical shifts | 39 | 36 | 92.3 |
13C chemical shifts | 80 | 73 | 91.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 148 | 128 | 86.5 |
15N chemical shifts | 5 | 0 | 0.0 |
13C chemical shifts | 86 | 67 | 77.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 11 | 8 | 72.7 |
13C chemical shifts | 11 | 8 | 72.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 22 | 20 | 90.9 |
13C chemical shifts | 20 | 10 | 50.0 |
Covalent bonds
Distance restraints
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK ||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||| .......SYRCPCRFFESHVARANVKHLKILNTP.CACQIVARLK..NRQVCIDPKLKWIQEYLEKCLNK
-100-----110-------120-------130-------- GSMEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK ||||||||||||||| |||||||||||||| | | ...EGISIYTSDNYTEEM..GDXDSMKEPAFREE...F.K
-200-----210-------220-------230-------240-------250-------260-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK ||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||| .......SYRCPCRFFESHVARANVKHLKILNTP.CACQIVARLK..NRQVCIDPKLKWIQEYLEKCLNK
-300-----310-------320-------330-------- GSMEGISIYTSDNYTEEMGSGDXDSMKEPAFREENANFNK ||||||||||||||| |||||||||||||| | | ...EGISIYTSDNYTEEM..GDXDSMKEPAFREE...F.K
Dihedral angle restraints
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK ||||||||||||||||||||||||||||| |||||| |||||| |||||||||| ........YRCPCRFFESHVARANVKHLKILNTPNCA.QIVARL....RQVCID...KWIQEYLEKC -0--------10--------20--------30--------40--------50--------60-----
-200-----210-------220-------230-------240-------250-------260-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK ||||||||||||||||||||||||||||| |||||| |||||| |||||||||| ........YRCPCRFFESHVARANVKHLKILNTPNCA.QIVARL....RQVCID...KWIQEYLEKC -200-----210-------220-------230-------240-------250-------260-----