PDB Short entry for 2N55 HEADER CYTOKINE/SIGNALING PROTEIN 07-JUL-15 2N55 TITLE STRUCTURE OF CONSTITUTIVELY MONOMERIC CXCL12 IN COMPLEX WITH THE CXCR4 TITLE 2 N-TERMINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMAL CELL-DERIVED FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SDF-1, HSDF-1, C-X-C MOTIF CHEMOKINE 12, INTERCRINE REDUCED COMPND 5 IN HEPATOMAS, IRH, HIRH, PRE-B CELL GROWTH-STIMULATING FACTOR, PBSF, COMPND 6 SDF-1-BETA(3-72), SDF-1-ALPHA(3-67); COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: C-X-C CHEMOKINE RECEPTOR TYPE 4; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: CXC-R4, CXCR-4, FB22, FUSIN, HM89, LCR1, LEUKOCYTE-DERIVED COMPND 13 SEVEN TRANSMEMBRANE DOMAIN RECEPTOR, LESTR, LIPOPOLYSACCHARIDE- COMPND 14 ASSOCIATED PROTEIN 3, LAP-3, LPS-ASSOCIATED PROTEIN 3, NPYRL, STROMAL COMPND 15 CELL-DERIVED FACTOR 1 RECEPTOR, SDF-1 RECEPTOR; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CXCL12, SDF1, SDF1A, SDF1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE30; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: CXCR4; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS CXL12, CXCR4, CHEMOKINE, GPCR, SDF1, CYTOKINE-SIGNALING PROTEIN KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.J.ZIAREK,F.C.PETERSON,B.F.VOLKMAN REVDAT 5 14-JUN-23 2N55 1 REMARK SEQADV REVDAT 4 03-MAY-17 2N55 1 JRNL REVDAT 3 25-MAY-16 2N55 1 JRNL REVDAT 2 11-MAY-16 2N55 1 JRNL REVDAT 1 27-APR-16 2N55 0 JRNL AUTH J.J.ZIAREK,A.B.KLEIST,N.LONDON,B.RAVEH,N.MONTPAS, JRNL AUTH 2 J.BONNETERRE,G.ST-ONGE,C.J.DICOSMO-PONTICELLO,C.A.KOPLINSKI, JRNL AUTH 3 I.ROY,B.STEPHENS,S.THELEN,C.T.VELDKAMP,F.D.COFFMAN, JRNL AUTH 4 M.C.COHEN,M.B.DWINELL,M.THELEN,F.C.PETERSON,N.HEVEKER, JRNL AUTH 5 B.F.VOLKMAN JRNL TITL STRUCTURAL BASIS FOR CHEMOKINE RECOGNITION BY A G JRNL TITL 2 PROTEIN-COUPLED RECEPTOR AND IMPLICATIONS FOR RECEPTOR JRNL TITL 3 ACTIVATION. JRNL REF SCI SIGNAL V. 10 2017 JRNL REFN ESSN 1937-9145 JRNL PMID 28325822 JRNL DOI 10.1126/SCISIGNAL.AAH5756 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CYANA, X-PLOR NIH REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000104434. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN_1, 25 MM [U-2H] MES, 10 % REMARK 210 [U-99% 2H] D2O, 0.02 % SODIUM REMARK 210 AZIDE, 2 MM PROTEIN_2, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-99% 13C; U-99% REMARK 210 15N] PROTEIN_2, 25 MM [U-2H] MES, REMARK 210 0.02 % SODIUM AZIDE, 10 % [U-99% REMARK 210 2H] D2O, 2 MM PROTEIN_1, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D F1-13C FILTERED/F3- REMARK 210 13C EDITED NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, NMRPIPE, GARANT, TOPSPIN, REMARK 210 X-PLOR NIH, TALOS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 4 164.89 67.96 REMARK 500 1 LEU A 5 -32.80 72.26 REMARK 500 1 ARG A 8 -80.78 -105.92 REMARK 500 1 CYS A 34 -89.45 -128.47 REMARK 500 1 LYS A 43 -70.59 -70.97 REMARK 500 1 MET B 201 -69.20 -148.59 REMARK 500 1 ILE B 204 -46.51 -130.71 REMARK 500 1 SER B 205 91.02 65.52 REMARK 500 1 ASN B 211 137.39 -175.79 REMARK 500 1 ALA B 228 -73.02 -128.54 REMARK 500 1 ARG B 230 78.35 51.10 REMARK 500 1 GLU B 231 -48.46 -169.57 REMARK 500 1 ASN B 235 -22.72 78.65 REMARK 500 2 SER A 6 75.90 60.25 REMARK 500 2 TYR A 7 25.70 -143.01 REMARK 500 2 ARG A 8 -171.26 79.96 REMARK 500 2 SER A 16 -72.57 -87.29 REMARK 500 2 ASN A 30 71.12 -105.69 REMARK 500 2 CYS A 34 -92.91 -142.71 REMARK 500 2 ASN A 46 -4.82 66.43 REMARK 500 2 LYS B 225 106.07 -167.27 REMARK 500 2 ALA B 228 -77.92 71.27 REMARK 500 2 PHE B 229 -73.84 -119.10 REMARK 500 2 ALA B 234 -80.63 65.86 REMARK 500 3 VAL A 3 -80.12 -71.92 REMARK 500 3 SER A 4 116.98 70.93 REMARK 500 3 ASN A 30 79.58 -103.77 REMARK 500 3 CYS A 34 -156.78 -149.34 REMARK 500 3 LYS A 43 -77.22 -68.91 REMARK 500 3 PRO A 53 19.19 -66.79 REMARK 500 3 MET B 201 83.01 60.56 REMARK 500 3 ILE B 204 -49.67 73.45 REMARK 500 3 SER B 205 90.95 62.72 REMARK 500 3 ASN B 211 147.33 -175.16 REMARK 500 3 LYS B 225 110.77 73.92 REMARK 500 3 ALA B 228 -54.97 -151.19 REMARK 500 3 PHE B 229 -67.04 -129.51 REMARK 500 3 ARG B 230 -39.32 173.18 REMARK 500 3 GLU B 231 -150.25 -140.86 REMARK 500 3 PHE B 236 88.93 62.62 REMARK 500 4 LEU A 5 125.09 64.41 REMARK 500 4 SER A 6 97.74 61.55 REMARK 500 4 ASN A 30 48.85 -91.67 REMARK 500 4 LYS A 43 -81.79 -71.29 REMARK 500 4 ASN A 46 -6.09 64.14 REMARK 500 4 SER B 200 76.72 67.50 REMARK 500 4 MET B 201 -65.97 -135.61 REMARK 500 4 GLU B 202 -62.37 -97.51 REMARK 500 4 ILE B 206 -154.50 -139.58 REMARK 500 4 SER B 218 114.49 72.32 REMARK 500 REMARK 500 THIS ENTRY HAS 259 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25694 RELATED DB: BMRB DBREF 2N55 A 1 68 UNP P48061 SDF1_HUMAN 22 89 DBREF 2N55 B 201 238 UNP P61073 CXCR4_HUMAN 1 38 SEQADV 2N55 GLY A -1 UNP P48061 EXPRESSION TAG SEQADV 2N55 MET A 0 UNP P48061 EXPRESSION TAG SEQADV 2N55 CYS A 55 UNP P48061 LEU 76 ENGINEERED MUTATION SEQADV 2N55 CYS A 58 UNP P48061 ILE 79 ENGINEERED MUTATION SEQADV 2N55 GLY B 199 UNP P61073 EXPRESSION TAG SEQADV 2N55 SER B 200 UNP P61073 EXPRESSION TAG SEQADV 2N55 ALA B 228 UNP P61073 CYS 28 ENGINEERED MUTATION SEQRES 1 A 70 GLY MET LYS PRO VAL SER LEU SER TYR ARG CYS PRO CYS SEQRES 2 A 70 ARG PHE PHE GLU SER HIS VAL ALA ARG ALA ASN VAL LYS SEQRES 3 A 70 HIS LEU LYS ILE LEU ASN THR PRO ASN CYS ALA LEU GLN SEQRES 4 A 70 ILE VAL ALA ARG LEU LYS ASN ASN ASN ARG GLN VAL CYS SEQRES 5 A 70 ILE ASP PRO LYS CYS LYS TRP CYS GLN GLU TYR LEU GLU SEQRES 6 A 70 LYS ALA LEU ASN LYS SEQRES 1 B 40 GLY SER MET GLU GLY ILE SER ILE TYR THR SER ASP ASN SEQRES 2 B 40 TYR THR GLU GLU MET GLY SER GLY ASP TYR ASP SER MET SEQRES 3 B 40 LYS GLU PRO ALA PHE ARG GLU GLU ASN ALA ASN PHE ASN SEQRES 4 B 40 LYS HELIX 1 1 ALA A 19 ALA A 21 5 3 HELIX 2 2 LYS A 56 LEU A 66 1 11 SHEET 1 A 4 GLN A 48 ILE A 51 0 SHEET 2 A 4 LEU A 36 LEU A 42 -1 N ALA A 40 O VAL A 49 SHEET 3 A 4 VAL A 23 ASN A 30 -1 N LEU A 29 O GLN A 37 SHEET 4 A 4 THR B 208 SER B 209 1 O SER B 209 N ILE A 28 SSBOND 1 CYS A 9 CYS A 34 1555 1555 2.03 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.02 SSBOND 3 CYS A 55 CYS A 58 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000