10 20 30 40 50 60 70 80 2KED - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER CYTOKINE 28-JAN-09 2KED
TITLE STRUCTURE OF SDF-1/CXCL12
COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMAL CELL-DERIVED FACTOR 1-ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SDF-1, C-X-C MOTIF CHEMOKINE 12, PRE-B CELL COMPND 5 GROWTH-STIMULATING FACTOR, PBSF, HIRH, SDF-1-ALPHA(3-67); COMPND 6 ENGINEERED: 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: PQE30
KEYWDS STROMAL CELL DERIVED FACTOR-1, SDF1-ALPHA, CXCL12, KEYWDS 2 CHEMOKINE, ALTERNATIVE SPLICING, CHEMOTAXIS, CYTOKINE, KEYWDS 3 GROWTH FACTOR, SECRETED
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR B.F.VOLKMAN,C.T.VELDKAMP,F.C.PETERSON
REVDAT 1 29-SEP-09 2KED 0
JRNL AUTH C.T.VELDKAMP,J.J.ZIAREK,J.SU,H.BASNET,R.LENNERTZ, JRNL AUTH 2 J.J.WEINER,F.C.PETERSON,J.E.BAKER,B.F.VOLKMAN JRNL TITL MONOMERIC STRUCTURE OF THE CARDIOPROTECTIVE JRNL TITL 2 CHEMOKINE SDF-1/CXCL12 JRNL REF PROTEIN SCI. V. 18 1359 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19551879 JRNL DOI 10.1002/PRO.167
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.3 REMARK 3 AUTHORS : SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N., REMARK 3 CLORE,G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTOMATED METHODS WERE USED FOR REMARK 3 BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REMARK 3 REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR REMARK 3 DYNAMICS IN EXPLICIT SOLVENT, CXCL12 STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1221 NOE CONSTRAINTS (371 INTRA, 239 SEQUENTIAL, 219 REMARK 3 MEDIUM, 392 LONG RANGE) AND 66 PHI AND PSI DIHEDRAL ANGLE REMARK 3 CONSTRAINTS.
REMARK 4 REMARK 4 2KED COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB101016.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0.001 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6 MM [U-100% 13C; U-100% REMARK 210 15N] CXCL12/SDF1-ALPHA, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_ REMARK 210 13C-SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY (AROMATIC) 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 : XWINNMR 3.5, NMRPIPE 2004, REMARK 210 XEASY 1.3, GARANT 2.1, CYANA REMARK 210 2.1 REMARK 210 METHOD USED : 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 MET A 0
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 VAL A 3 73.94 66.91 REMARK 500 1 SER A 4 114.91 -174.37 REMARK 500 1 SER A 6 73.00 53.82 REMARK 500 1 HIS A 17 81.43 61.07 REMARK 500 1 PRO A 32 -60.14 -27.84 REMARK 500 1 ALA A 35 -166.41 68.03 REMARK 500 1 LYS A 43 -71.54 -72.38 REMARK 500 1 ASN A 46 17.85 59.73 REMARK 500 1 LYS A 64 -70.18 -58.56 REMARK 500 2 ALA A 35 -167.76 62.54 REMARK 500 2 LYS A 64 -71.05 -58.03 REMARK 500 3 VAL A 3 -75.56 69.10 REMARK 500 3 PRO A 32 -29.18 -28.15 REMARK 500 3 ASN A 33 28.71 -162.64 REMARK 500 3 ALA A 35 179.47 174.24 REMARK 500 3 LYS A 43 -71.63 -70.91 REMARK 500 4 SER A 4 31.26 -84.75 REMARK 500 4 ASN A 33 -38.74 -130.98 REMARK 500 4 ALA A 35 -164.63 65.72 REMARK 500 5 ALA A 35 -167.30 67.62 REMARK 500 6 PRO A 32 -60.35 -29.46 REMARK 500 6 ALA A 35 -92.10 67.43 REMARK 500 6 LYS A 64 -71.25 -53.91 REMARK 500 7 ARG A 12 -32.66 -130.65 REMARK 500 7 ALA A 35 -163.45 64.02 REMARK 500 8 LEU A 5 80.98 -156.84 REMARK 500 8 PRO A 32 2.99 -55.28 REMARK 500 8 CYS A 34 -73.60 -133.29 REMARK 500 8 ALA A 35 -172.13 163.92 REMARK 500 8 ASN A 46 -5.27 70.05 REMARK 500 9 PRO A 32 -16.98 -42.43 REMARK 500 9 ASN A 33 10.31 -146.96 REMARK 500 9 ALA A 35 -168.53 67.92 REMARK 500 10 TYR A 7 -63.03 -98.86 REMARK 500 10 PRO A 32 25.20 -74.68 REMARK 500 10 CYS A 34 -69.92 -136.03 REMARK 500 10 ALA A 35 -177.42 165.94 REMARK 500 11 SER A 4 80.16 58.61 REMARK 500 11 ASN A 33 -14.37 77.26 REMARK 500 11 ALA A 35 -173.63 67.56 REMARK 500 11 PRO A 53 2.25 -68.76 REMARK 500 12 SER A 6 172.46 68.09 REMARK 500 12 ALA A 35 -169.42 69.29 REMARK 500 12 ASN A 46 -6.65 66.35 REMARK 500 13 LEU A 5 107.87 66.86 REMARK 500 13 PRO A 32 -61.93 -27.69 REMARK 500 13 ALA A 35 -167.19 69.06 REMARK 500 14 SER A 4 78.62 74.11 REMARK 500 14 SER A 6 -167.30 61.96 REMARK 500 14 HIS A 17 88.31 -154.89 REMARK 500 14 PRO A 32 -51.97 -29.03 REMARK 500 14 ALA A 35 -167.35 66.16 REMARK 500 14 ASN A 46 -0.81 70.12 REMARK 500 15 ALA A 35 -163.65 70.45 REMARK 500 15 ASN A 46 -0.67 62.59 REMARK 500 16 PRO A 2 90.79 -69.30 REMARK 500 16 VAL A 3 116.98 -174.82 REMARK 500 16 PRO A 32 -40.02 -29.62 REMARK 500 16 ASN A 33 12.44 -141.96 REMARK 500 16 ALA A 35 -167.76 63.28 REMARK 500 16 ASN A 46 -9.92 66.01 REMARK 500 16 LYS A 64 -70.05 -60.74 REMARK 500 17 LEU A 5 61.99 -169.24 REMARK 500 17 ALA A 35 -163.83 68.15 REMARK 500 18 PRO A 32 -31.95 -39.28 REMARK 500 18 ALA A 35 -161.37 68.13 REMARK 500 18 LYS A 64 -70.76 -57.56 REMARK 500 19 ALA A 35 -171.48 69.75 REMARK 500 20 VAL A 3 -38.02 -160.58 REMARK 500 20 PRO A 32 19.03 -62.06 REMARK 500 20 ASN A 33 -32.99 -174.82 REMARK 500 20 CYS A 34 -75.17 -71.10 REMARK 500 20 ALA A 35 -169.12 176.11 REMARK 500 20 ASN A 46 -8.06 67.14 REMARK 500 20 LYS A 64 -73.84 -61.99 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16143 RELATED DB: BMRB REMARK 900 RELATED ID: 2KED RELATED DB: PDB REMARK 900 RELATED ID: 2KEE RELATED DB: PDB
DBREF 2KED A 1 68 UNP P48061 SDF1_HUMAN 22 89
SEQADV 2KED GLY A -1 UNP P48061 EXPRESSION TAG SEQADV 2KED MET A 0 UNP P48061 EXPRESSION TAG
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 LEU LYS TRP ILE GLN GLU TYR LEU GLU SEQRES 6 A 70 LYS ALA LEU ASN LYS
HELIX 1 1 LEU A 55 LYS A 68 1 14
SHEET 1 A 3 VAL A 23 THR A 31 0 SHEET 2 A 3 ALA A 35 LEU A 42 -1 O GLN A 37 N LEU A 29 SHEET 3 A 3 GLN A 48 ILE A 51 -1 O VAL A 49 N ALA A 40
SSBOND 1 CYS A 9 CYS A 34 1555 1555 2.00 SSBOND 2 CYS A 11 CYS A 50 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