1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Ziarek, J.J. Peterson, F.C. Volkman, B.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Sci Signal 1937-9145 10 10.1126/scisignal.aah5756 28325822 Structural basis for chemokine recognition by a G protein-coupled receptor and implications for receptor activation. 2017 10.2210/pdb2n55/pdb pdb_00002n55 8146.680 Stromal cell-derived factor 1 L76C, I79C 1 man polymer 4518.772 C-X-C chemokine receptor type 4 C28A 1 man polymer SDF-1, hSDF-1, C-X-C motif chemokine 12, Intercrine reduced in hepatomas, IRH, hIRH, Pre-B cell growth-stimulating factor, PBSF, SDF-1-beta(3-72), SDF-1-alpha(3-67) CXC-R4, CXCR-4, FB22, Fusin, HM89, LCR1, Leukocyte-derived seven transmembrane domain receptor, LESTR, Lipopolysaccharide-associated protein 3, LAP-3, LPS-associated protein 3, NPYRL, Stromal cell-derived factor 1 receptor, SDF-1 receptor no no GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKCKWCQEYLEKALNK GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKCKWCQEYLEKALNK A polypeptide(L) no no GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK GSMEGISIYTSDNYTEEMGSGDYDSMKEPAFREENANFNK B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample CXCL12, SDF1, SDF1A, SDF1B 9606 Homo sapiens 562 Escherichia coli plasmid pQE30 human sample CXCR4 9606 Homo sapiens 562 Escherichia coli plasmid pQE30 database_2 pdbx_database_status pdbx_nmr_software struct_ref_seq_dif repository Initial release Database references Database references Database references Data collection Database references Other 1 0 2016-04-27 1 1 2016-05-11 1 2 2016-05-25 1 3 2017-05-03 1 4 2023-06-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data _pdbx_nmr_software.name _struct_ref_seq_dif.details BMRB Y RCSB 2015-07-07 REL REL REL REL 1533 365 486 241 441 57 52 target function 100 20 1 3D 1H-15N NOESY 3D 1H-13C NOESY aliphatic 3D 1H-13C NOESY aromatic 3D 1H-15N NOESY 3D 1H-13C NOESY aliphatic 3D 1H-13C NOESY aromatic 3D F1-13C filtered/F3-13C edited NOESY aliphatic 3D F1-13C filtered/F3-13C edited NOESY aliphatic 2 mM [U-99% 13C; U-99% 15N] 25 mM [U-2H] 10 % [U-99% 2H] 0.02 % 2 mM 1 mM [U-99% 13C; U-99% 15N] 25 mM [U-2H] 0.02 % 10 % [U-99% 2H] 2 mM 0.02 6.8 ambient 298 K torsion angle dynamics, molecular dynamics 1 lowest energy 2 mM [U-99% 13C; U-99% 15N] protein_1, 25 mM [U-2H] MES, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 2 mM protein_2, 90% H2O/10% D2O 90% H2O/10% D2O 1 mM [U-99% 13C; U-99% 15N] protein_2, 25 mM [U-2H] MES, 0.02 % sodium azide, 10 % [U-99% 2H] D2O, 2 mM protein_1, 90% H2O/10% D2O 90% H2O/10% D2O Guntert, Mumenthaler and Wuthrich structure solution CYANA Guntert, Mumenthaler and Wuthrich refinement CYANA Bartels et al. chemical shift assignment XEASY Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Bartels, Guntert, Billeter and Wuthrich chemical shift assignment GARANT Bruker Biospin collection TopSpin Schwieters, Kuszewski, Tjandra and Clore geometry optimization X-PLOR NIH Cornilescu, Delaglio and Bax data analysis TALOS refinement X-PLOR NIH 600 Bruker DRX Bruker DRX GLY -1 n 1 GLY -1 A MET 0 n 2 MET 0 A LYS 1 n 3 LYS 1 A PRO 2 n 4 PRO 2 A VAL 3 n 5 VAL 3 A SER 4 n 6 SER 4 A LEU 5 n 7 LEU 5 A SER 6 n 8 SER 6 A TYR 7 n 9 TYR 7 A ARG 8 n 10 ARG 8 A CYS 9 n 11 CYS 9 A PRO 10 n 12 PRO 10 A CYS 11 n 13 CYS 11 A ARG 12 n 14 ARG 12 A PHE 13 n 15 PHE 13 A PHE 14 n 16 PHE 14 A GLU 15 n 17 GLU 15 A SER 16 n 18 SER 16 A HIS 17 n 19 HIS 17 A VAL 18 n 20 VAL 18 A ALA 19 n 21 ALA 19 A ARG 20 n 22 ARG 20 A ALA 21 n 23 ALA 21 A ASN 22 n 24 ASN 22 A VAL 23 n 25 VAL 23 A LYS 24 n 26 LYS 24 A HIS 25 n 27 HIS 25 A LEU 26 n 28 LEU 26 A LYS 27 n 29 LYS 27 A ILE 28 n 30 ILE 28 A LEU 29 n 31 LEU 29 A ASN 30 n 32 ASN 30 A THR 31 n 33 THR 31 A PRO 32 n 34 PRO 32 A ASN 33 n 35 ASN 33 A CYS 34 n 36 CYS 34 A ALA 35 n 37 ALA 35 A LEU 36 n 38 LEU 36 A GLN 37 n 39 GLN 37 A ILE 38 n 40 ILE 38 A VAL 39 n 41 VAL 39 A ALA 40 n 42 ALA 40 A ARG 41 n 43 ARG 41 A LEU 42 n 44 LEU 42 A LYS 43 n 45 LYS 43 A ASN 44 n 46 ASN 44 A ASN 45 n 47 ASN 45 A ASN 46 n 48 ASN 46 A ARG 47 n 49 ARG 47 A GLN 48 n 50 GLN 48 A VAL 49 n 51 VAL 49 A CYS 50 n 52 CYS 50 A ILE 51 n 53 ILE 51 A ASP 52 n 54 ASP 52 A PRO 53 n 55 PRO 53 A LYS 54 n 56 LYS 54 A CYS 55 n 57 CYS 55 A LYS 56 n 58 LYS 56 A TRP 57 n 59 TRP 57 A CYS 58 n 60 CYS 58 A GLN 59 n 61 GLN 59 A GLU 60 n 62 GLU 60 A TYR 61 n 63 TYR 61 A LEU 62 n 64 LEU 62 A GLU 63 n 65 GLU 63 A LYS 64 n 66 LYS 64 A ALA 65 n 67 ALA 65 A LEU 66 n 68 LEU 66 A ASN 67 n 69 ASN 67 A LYS 68 n 70 LYS 68 A GLY 199 n 1 GLY 199 B SER 200 n 2 SER 200 B MET 201 n 3 MET 201 B GLU 202 n 4 GLU 202 B GLY 203 n 5 GLY 203 B ILE 204 n 6 ILE 204 B SER 205 n 7 SER 205 B ILE 206 n 8 ILE 206 B TYR 207 n 9 TYR 207 B THR 208 n 10 THR 208 B SER 209 n 11 SER 209 B ASP 210 n 12 ASP 210 B ASN 211 n 13 ASN 211 B TYR 212 n 14 TYR 212 B THR 213 n 15 THR 213 B GLU 214 n 16 GLU 214 B GLU 215 n 17 GLU 215 B MET 216 n 18 MET 216 B GLY 217 n 19 GLY 217 B SER 218 n 20 SER 218 B GLY 219 n 21 GLY 219 B ASP 220 n 22 ASP 220 B TYR 221 n 23 TYR 221 B ASP 222 n 24 ASP 222 B SER 223 n 25 SER 223 B MET 224 n 26 MET 224 B LYS 225 n 27 LYS 225 B GLU 226 n 28 GLU 226 B PRO 227 n 29 PRO 227 B ALA 228 n 30 ALA 228 B PHE 229 n 31 PHE 229 B ARG 230 n 32 ARG 230 B GLU 231 n 33 GLU 231 B GLU 232 n 34 GLU 232 B ASN 233 n 35 ASN 233 B ALA 234 n 36 ALA 234 B ASN 235 n 37 ASN 235 B PHE 236 n 38 PHE 236 B ASN 237 n 39 ASN 237 B LYS 238 n 40 LYS 238 B author_defined_assembly 2 dimeric 3281.2 -10.4 7408.4 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O VAL 49 A O VAL 51 A N ALA 40 A N ALA 42 A O GLN 37 A O GLN 39 A N LEU 29 A N LEU 31 A N ILE 28 A N ILE 30 B O SER 209 B O SER 11 4 A B HZ1 OE1 LYS GLU 54 226 1.56 4 A B HG O SER LYS 16 225 1.59 4 A B HZ3 OE2 LYS GLU 56 231 1.59 6 A B HZ2 OE1 LYS GLU 27 214 1.59 17 A A OD1 HZ2 ASP LYS 52 54 1.58 1 A SER 4 67.96 164.89 1 A LEU 5 72.26 -32.80 1 A ARG 8 -105.92 -80.78 1 A CYS 34 -128.47 -89.45 1 A LYS 43 -70.97 -70.59 1 B MET 201 -148.59 -69.20 1 B ILE 204 -130.71 -46.51 1 B SER 205 65.52 91.02 1 B ASN 211 -175.79 137.39 1 B ALA 228 -128.54 -73.02 1 B ARG 230 51.10 78.35 1 B GLU 231 -169.57 -48.46 1 B ASN 235 78.65 -22.72 2 A SER 6 60.25 75.90 2 A TYR 7 -143.01 25.70 2 A ARG 8 79.96 -171.26 2 A SER 16 -87.29 -72.57 2 A ASN 30 -105.69 71.12 2 A CYS 34 -142.71 -92.91 2 A ASN 46 66.43 -4.82 2 B LYS 225 -167.27 106.07 2 B ALA 228 71.27 -77.92 2 B PHE 229 -119.10 -73.84 2 B ALA 234 65.86 -80.63 3 A VAL 3 -71.92 -80.12 3 A SER 4 70.93 116.98 3 A ASN 30 -103.77 79.58 3 A CYS 34 -149.34 -156.78 3 A LYS 43 -68.91 -77.22 3 A PRO 53 -66.79 19.19 3 B MET 201 60.56 83.01 3 B ILE 204 73.45 -49.67 3 B SER 205 62.72 90.95 3 B ASN 211 -175.16 147.33 3 B LYS 225 73.92 110.77 3 B ALA 228 -151.19 -54.97 3 B PHE 229 -129.51 -67.04 3 B ARG 230 173.18 -39.32 3 B GLU 231 -140.86 -150.25 3 B PHE 236 62.62 88.93 4 A LEU 5 64.41 125.09 4 A SER 6 61.55 97.74 4 A ASN 30 -91.67 48.85 4 A LYS 43 -71.29 -81.79 4 A ASN 46 64.14 -6.09 4 B SER 200 67.50 76.72 4 B MET 201 -135.61 -65.97 4 B GLU 202 -97.51 -62.37 4 B ILE 206 -139.58 -154.50 4 B SER 218 72.32 114.49 4 B SER 223 -63.53 16.00 4 B LYS 225 -177.85 103.51 4 B ALA 228 173.77 -68.95 4 B GLU 232 -90.51 -67.59 4 B ALA 234 -59.73 97.99 5 A ARG 8 -99.17 -72.95 5 A CYS 34 -129.67 -98.06 5 A LYS 43 -72.84 -72.19 5 B ILE 206 -133.23 -159.57 5 B ASN 211 175.39 158.14 5 B TYR 212 -138.07 -154.28 5 B THR 213 -140.69 16.82 5 B ARG 230 71.18 -50.48 5 B ASN 233 75.86 100.08 5 B ASN 237 -87.40 -72.73 6 A ARG 8 -66.38 -88.64 6 A ARG 12 -100.75 -67.19 6 A LYS 43 -70.52 -78.15 6 A ASN 46 62.50 -3.35 6 A CYS 55 -67.90 -176.49 6 B GLU 202 -145.89 -37.89 6 B SER 205 47.55 87.32 6 B ILE 206 -125.75 -161.25 6 B ASN 211 176.06 153.78 6 B SER 218 165.07 -174.68 6 B LYS 225 177.42 105.94 6 B ALA 234 62.41 -165.72 7 A LEU 29 -107.35 75.19 7 A ALA 35 -94.31 -156.76 7 A LYS 43 -69.72 -78.96 7 A CYS 55 -58.94 171.21 7 B SER 200 -166.78 -51.59 7 B SER 205 64.99 87.07 7 B TYR 212 -151.74 -84.23 7 B THR 213 -162.58 -70.88 7 B LYS 225 70.24 100.95 7 B PHE 229 -153.14 -74.21 7 B ARG 230 163.47 -37.94 8 A VAL 3 65.81 95.87 8 A ARG 8 65.32 -71.28 8 A HIS 17 45.12 79.64 8 A ASN 46 59.16 19.77 8 B MET 201 69.63 92.32 8 B ILE 204 -139.08 -51.83 8 B SER 205 63.88 99.15 8 B THR 213 -143.00 -32.81 8 B MET 224 -87.00 -88.49 8 B PRO 227 -62.22 -174.84 8 B GLU 231 56.16 -39.36 8 B GLU 232 -58.09 -71.38 8 B ASN 235 -165.74 110.52 8 B ASN 237 -155.30 83.74 9 A ARG 8 69.53 174.01 9 A LYS 43 -64.71 -89.12 9 B ILE 204 -140.60 -45.67 9 B SER 205 64.85 96.86 9 B PRO 227 -84.28 -74.56 9 B ALA 228 66.31 -72.26 9 B PHE 229 -164.02 -52.82 9 B ARG 230 73.53 72.12 9 B GLU 231 -173.67 -148.38 9 B GLU 232 -86.80 -79.18 9 B ALA 234 58.61 4.95 9 B PHE 236 -172.50 -39.05 9 B ASN 237 72.45 84.36 10 A SER 4 -98.56 48.28 10 A TYR 7 -170.09 -58.50 10 A ARG 8 176.68 -179.75 10 A CYS 34 -131.85 -96.59 10 A LYS 43 -70.46 -80.66 10 B ILE 206 -119.13 -152.44 10 B SER 223 27.94 -99.16 10 B MET 224 -179.26 -168.63 10 B PRO 227 -67.61 83.39 10 B ALA 228 63.05 -73.30 10 B PHE 229 -159.84 -15.48 10 B ARG 230 68.38 -73.91 10 B ASN 237 64.56 -177.35 11 A SER 4 -147.93 36.75 11 A ARG 8 -160.91 -165.47 11 A CYS 34 -139.65 -96.67 11 A LYS 43 -70.16 -75.85 11 A ASN 46 48.47 81.42 11 B ILE 206 -126.79 -154.65 11 B ASN 211 173.72 162.39 11 B SER 218 70.40 115.86 11 B MET 224 -122.69 -160.93 11 B PRO 227 -72.38 -158.73 11 B PHE 229 -145.27 -38.30 11 B ARG 230 69.77 -50.86 12 A PRO 2 -76.92 24.50 12 A SER 6 64.08 92.08 12 A ARG 8 64.74 -89.10 12 A ASN 30 -100.27 44.12 12 A CYS 34 -124.31 -97.38 12 A LYS 43 -69.17 -77.15 12 A PRO 53 -69.61 8.89 12 B SER 218 85.03 177.90 12 B LYS 225 67.15 98.95 12 B ARG 230 62.35 -82.56 13 A MET 0 62.68 98.14 13 A VAL 3 65.89 -84.22 13 A SER 4 61.81 -176.25 13 A ARG 12 -101.83 -60.93 13 A CYS 34 -105.08 -94.54 13 A CYS 55 -72.36 -166.10 13 B ASN 211 165.13 167.54 13 B SER 223 -58.75 43.28 13 B LYS 225 78.03 76.40 13 B ALA 234 64.56 -164.53 13 B ASN 237 69.72 -79.01 14 A PRO 2 -55.81 172.88 14 A VAL 3 73.78 108.44 14 A LEU 5 67.88 91.70 14 A SER 6 -78.56 26.77 14 A TYR 7 -172.69 -166.22 14 A ASN 30 -104.15 79.79 14 A LYS 43 -56.58 -78.15 14 A ASN 46 58.99 15.27 14 A PRO 53 -69.27 3.80 14 B ILE 206 -133.34 -149.27 14 B SER 218 -102.77 -69.53 14 B LYS 225 -178.86 105.24 14 B ALA 228 66.98 -54.69 14 B ARG 230 -173.68 -71.74 14 B GLU 231 -154.46 -61.36 14 B ASN 233 171.57 -167.78 14 B ASN 237 67.18 -63.57 15 A PRO 2 -59.18 104.24 15 A VAL 3 -148.34 -28.41 15 A CYS 34 -103.88 -97.93 15 A PRO 53 -63.87 7.38 15 B SER 205 68.54 78.34 15 B SER 218 -163.04 116.06 15 B SER 223 73.34 66.96 15 B LYS 225 -159.05 17.79 15 B PHE 229 -136.72 -34.59 15 B ARG 230 45.42 73.44 15 B ASN 233 -147.13 -51.89 16 A LYS 1 76.32 137.64 16 A TYR 7 79.01 113.87 16 A ARG 8 -132.16 -73.79 16 A HIS 17 -154.27 88.37 16 A CYS 34 -135.48 -93.75 16 A PRO 53 -67.24 22.90 16 B GLU 202 -172.97 -26.84 16 B ILE 206 -129.42 -165.71 16 B LYS 225 -170.25 90.31 16 B ALA 228 168.60 15.63 16 B PHE 229 -135.96 -75.99 16 B ARG 230 -178.12 -43.19 16 B GLU 231 -152.26 -44.13 16 B ALA 234 -167.21 -19.82 17 A SER 4 70.24 113.06 17 A ARG 8 -118.00 -80.09 17 A SER 16 -75.75 -72.52 17 A CYS 34 -121.23 -93.02 17 A LYS 43 -69.96 -76.78 17 B THR 213 -144.11 13.04 17 B LYS 225 -168.42 89.66 17 B ALA 228 64.94 -81.78 17 B PHE 229 -148.42 20.43 17 B ARG 230 -57.43 105.26 17 B GLU 231 -141.46 -76.41 17 B GLU 232 -90.58 -64.05 17 B PHE 236 68.62 -67.42 17 B ASN 237 70.89 124.16 18 A LEU 5 68.86 -89.58 18 A ARG 8 176.31 161.57 18 A HIS 17 49.59 75.07 18 A LYS 43 -70.17 -79.32 18 B MET 201 70.31 140.61 18 B SER 205 69.34 -71.35 18 B ILE 206 44.57 -146.21 18 B THR 213 -139.64 -54.05 18 B SER 218 -162.40 100.10 18 B SER 223 -68.33 99.80 18 B LYS 225 71.64 96.24 18 B PHE 229 -151.49 -73.73 18 B ARG 230 59.89 -82.69 18 B ASN 233 73.39 -57.04 18 B ALA 234 168.95 -53.23 18 B ASN 235 176.04 133.00 18 B ASN 237 73.41 112.44 19 A LEU 5 -177.15 -68.29 19 A TYR 7 -140.56 22.51 19 A ARG 8 73.98 175.49 19 A HIS 17 -152.80 85.37 19 A CYS 34 -159.56 -157.36 19 A LYS 43 -58.81 -89.58 19 A ASN 46 62.25 88.64 19 A PRO 53 -64.36 8.31 19 B MET 201 59.08 81.79 19 B ILE 206 -135.42 -155.96 19 B TYR 221 -64.14 98.96 19 B LYS 225 77.84 98.22 19 B ALA 228 167.08 -70.45 19 B ARG 230 70.84 -47.75 20 A ARG 8 67.33 -168.06 20 A CYS 34 -101.41 -94.63 20 A LYS 43 -70.48 -79.82 20 A LEU 66 -65.87 6.81 20 B SER 200 69.24 99.98 20 B SER 205 43.42 79.61 20 B SER 218 65.38 113.59 20 B SER 223 77.96 67.63 20 B PHE 229 173.75 -28.08 20 B ARG 230 69.62 -62.31 20 B ALA 234 -138.39 -47.72 lowest energy, model1 Structure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus 1 N N 2 N N A ALA 19 A ALA 21 HELX_P A ALA 21 A ALA 23 5 1 3 A LYS 56 A LYS 58 HELX_P A LEU 66 A LEU 68 1 2 11 disulf 2.027 A CYS 9 A SG CYS 11 1_555 A CYS 34 A SG CYS 36 1_555 disulf 2.015 A CYS 11 A SG CYS 13 1_555 A CYS 50 A SG CYS 52 1_555 disulf 2.028 A CYS 55 A SG CYS 57 1_555 A CYS 58 A SG CYS 60 1_555 CYTOKINE/Signaling Protein CXL12, CXCR4, chemokine, GPCR, SDF1, CYTOKINE-Signaling Protein complex SDF1_HUMAN UNP 1 22 P48061 KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK CXCR4_HUMAN UNP 2 1 P61073 MEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNK 22 89 2N55 1 68 P48061 A 1 3 70 1 38 2N55 201 238 P61073 B 2 3 40 1 expression tag GLY -1 2N55 A P48061 UNP 1 1 expression tag MET 0 2N55 A P48061 UNP 2 1 LEU engineered mutation CYS 55 2N55 A P48061 UNP 76 57 1 ILE engineered mutation CYS 58 2N55 A P48061 UNP 79 60 2 expression tag GLY 199 2N55 B P61073 UNP 1 2 expression tag SER 200 2N55 B P61073 UNP 2 2 CYS engineered mutation ALA 228 2N55 B P61073 UNP 28 30 4 anti-parallel anti-parallel parallel A GLN 48 A GLN 50 A ILE 51 A ILE 53 A LEU 36 A LEU 38 A LEU 42 A LEU 44 A VAL 23 A VAL 25 A ASN 30 A ASN 32 B THR 208 B THR 10 B SER 209 B SER 11