Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
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 | 89.8 % (1177 of 1310) | 90.8 % (628 of 692) | 88.2 % (439 of 498) | 91.7 % (110 of 120) |
Backbone | 94.2 % (612 of 650) | 94.5 % (208 of 220) | 93.2 % (303 of 325) | 96.2 % (101 of 105) |
Sidechain | 86.8 % (664 of 765) | 89.0 % (420 of 472) | 84.5 % (235 of 278) | 60.0 % (9 of 15) |
Aromatic | 74.0 % (74 of 100) | 92.0 % (46 of 50) | 55.1 % (27 of 49) | 100.0 % (1 of 1) |
Methyl | 95.6 % (86 of 90) | 97.8 % (44 of 45) | 93.3 % (42 of 45) |
1. CXCL12/SDF1-alpha
GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCACQI VARLKNNNRQ VCIDPKLKWI QEYLEKCLNK2. CXCR4
GSMEGISIYT SDNYTEEMGS GDYDSMKEPA FREENANFNKSolvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.310 mM CXCL12 U-15N/13C (dimer concentration), 0.775 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | .31 mM | |
2 | CXCR4 | natural abundance | .775 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 1.0 mM CXCR4 U-15N/13C, 0.625 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.0 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.625 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 0.310 mM CXCL12 U-15N/13C (dimer concentration), 0.775 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | .31 mM | |
2 | CXCR4 | natural abundance | .775 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 0.310 mM CXCL12 U-15N/13C (dimer concentration), 0.775 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | .31 mM | |
2 | CXCR4 | natural abundance | .775 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 0.310 mM CXCL12 U-15N/13C (dimer concentration), 0.775 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | .31 mM | |
2 | CXCR4 | natural abundance | .775 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 0.310 mM CXCL12 U-15N/13C (dimer concentration), 0.775 mM unlabled CXCR4, 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | .31 mM | |
2 | CXCR4 | natural abundance | .775 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 1.0 mM CXCR4 U-15N/13C, 0.625 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.0 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.625 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 1.0 mM CXCR4 U-15N/13C, 0.625 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.0 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.625 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 1.0 mM CXCR4 U-15N/13C, 0.625 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.0 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.625 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 1.0 mM CXCR4 U-15N/13C, 0.625 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CXCR4 | [U-100% 13C; U-100% 15N] | 1.0 mM | |
7 | CXCL12/SDF1-alpha | natural abundance | 0.625 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_15636_2k04.nef |
Input source #2: Coordindates | 2k04.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 (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 | 2.014 |
A:11:CYS:SG | A:50:CYS:SG | unknown | oxidized, CA 58.054, CB 43.375 ppm | 2.008 |
A:36:CYS:SG | C:265:CYS:SG | oxidized, CA 58.616, CB 45.705 ppm | unknown | 2.041 |
A:65:CYS:SG | C:236:CYS:SG | oxidized, CA 56.329, CB 45.235 ppm | unknown | 2.039 |
C:209:CYS:SG | C:234:CYS:SG | unknown | unknown | 2.032 |
C:211:CYS:SG | C:250:CYS:SG | unknown | unknown | 2.028 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK --------10--------20--------30--------40--------50--------60--------70
-100-----110-------120-------130-------- GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK |||||||||||||||||||||||||||||||||||||||| GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK --------10--------20--------30--------40
-200-----210-------220-------230-------240-------250-------260-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK --------10--------20--------30--------40--------50--------60--------70
-300-----310-------320-------330-------- GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK |||||||||||||||||||||||||||||||||||||||| GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK --------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_15636_2k04.nef
Assigned chemical shifts
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ..KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLK..NRQVCIDPKLKWIQEYLEKCLNK
-100-----110-------120-------130-------- GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK |||||||||||||||||||||||||||||||||||||| ..MEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK
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 | 168 | 140 | 83.3 |
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 | 88 | 67 | 76.1 |
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 | 22 | 10 | 45.5 |
Covalent bonds
Distance restraints
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||| ......LSYRCPCRFFESHVARANVKHLKILNTP.CACQIVARLK..NRQVCIDPKLKWIQEYLEKCLNK
-100-----110-------120-------130-------- GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK |||||||||||||||| |||||||||||||| | | ...EGISIYTSDNYTEEMG.GDYDSMKEPAFREE...F.K
-200-----210-------220-------230-------240-------250-------260-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||| ......LSYRCPCRFFESHVARANVKHLKILNTP.CACQIVARLK..NRQVCIDPKLKWIQEYLEKCLNK
-300-----310-------320-------330-------- GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK |||||||||||||||| |||||||||||||| | | ...EGISIYTSDNYTEEMG.GDYDSMKEPAFREE...F.K
Dihedral angle restraints
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||| |||||||||||||||||| |||||| |||||| |||||||||| ........YRCPCRFFES.VARANVKHLKILNTPNCA.QIVARL....RQVCID...KWIQEYLEKC -0--------10--------20--------30--------40--------50--------60-----
-200-----210-------220-------230-------240-------250-------260-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK |||||||||| |||||||||||||||||| |||||| |||||| |||||||||| ........YRCPCRFFES.VARANVKHLKILNTPNCA.QIVARL....RQVCID...KWIQEYLEKC -200-----210-------220-------230-------240-------250-------260-----