HEADER CYTOKINE 28-JAN-09 2KEE 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 GROWTH- COMPND 5 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, CHEMOKINE, KEYWDS 2 ALTERNATIVE SPLICING, CHEMOTAXIS, CYTOKINE, GROWTH FACTOR, SECRETED EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.F.VOLKMAN,C.T.VELDKAMP,F.C.PETERSON REVDAT 3 14-JUN-23 2KEE 1 REMARK REVDAT 2 19-FEB-20 2KEE 1 REMARK SEQADV REVDAT 1 29-SEP-09 2KEE 0 JRNL AUTH C.T.VELDKAMP,J.J.ZIAREK,J.SU,H.BASNET,R.LENNERTZ,J.J.WEINER, JRNL AUTH 2 F.C.PETERSON,J.E.BAKER,B.F.VOLKMAN JRNL TITL MONOMERIC STRUCTURE OF THE CARDIOPROTECTIVE CHEMOKINE JRNL TITL 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.9.3 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTOMATED METHODS WERE USED FOR REMARK 3 BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. REMARK 3 FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT REMARK 3 SOLVENT, CXCL12 STRUCTURES ARE BASED ON A TOTAL OF 1140 NOE REMARK 3 CONSTRAINTS ( 393 INTRA, 239 SEQUENTIAL, 168 MEDIUM, 340 LONG REMARK 3 RANGE) AND 50 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. REMARK 4 REMARK 4 2KEE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000101017. 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 : 0.001 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM CXCL12/SDF1-ALPHA, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -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 : TOPSPIN, NMRPIPE 2004, XEASY REMARK 210 1.3, CYANA 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 SER A 0 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 H LYS A 24 O ARG A 41 1.60 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 LEU A 5 -70.23 67.59 REMARK 500 1 ARG A 8 -86.36 67.98 REMARK 500 1 SER A 16 -42.10 69.13 REMARK 500 1 CYS A 34 -78.19 -142.83 REMARK 500 1 ALA A 35 -168.48 175.24 REMARK 500 2 ARG A 8 -71.65 68.52 REMARK 500 2 SER A 16 -31.26 70.93 REMARK 500 2 HIS A 17 32.74 -90.76 REMARK 500 2 ALA A 35 -164.86 64.59 REMARK 500 3 SER A 4 85.16 61.43 REMARK 500 3 SER A 6 -173.88 69.86 REMARK 500 3 PRO A 10 -54.99 -23.64 REMARK 500 3 HIS A 17 30.39 -144.72 REMARK 500 3 CYS A 34 -80.12 -126.90 REMARK 500 3 ALA A 35 -167.94 170.65 REMARK 500 4 SER A 6 103.91 66.65 REMARK 500 4 CYS A 34 10.06 -142.74 REMARK 500 4 ALA A 35 -154.57 64.69 REMARK 500 5 SER A 4 -30.53 -144.32 REMARK 500 5 LEU A 5 66.90 62.58 REMARK 500 5 SER A 16 -0.94 56.65 REMARK 500 5 CYS A 34 -79.54 -114.41 REMARK 500 5 ALA A 35 -177.51 165.65 REMARK 500 6 ARG A 8 -70.55 -59.44 REMARK 500 6 SER A 16 -4.22 71.87 REMARK 500 7 SER A 4 -64.16 70.90 REMARK 500 7 LEU A 5 79.22 50.98 REMARK 500 7 ARG A 8 -61.49 -99.13 REMARK 500 7 SER A 16 -23.33 64.22 REMARK 500 7 HIS A 17 32.96 -95.34 REMARK 500 7 ALA A 35 -163.63 66.60 REMARK 500 8 CYS A 34 19.19 -141.33 REMARK 500 8 ALA A 35 178.88 69.93 REMARK 500 8 ASN A 46 -7.85 69.70 REMARK 500 9 SER A 4 -22.44 -146.09 REMARK 500 9 LEU A 5 -77.10 67.84 REMARK 500 9 SER A 6 129.45 -171.22 REMARK 500 9 SER A 16 -5.66 62.84 REMARK 500 9 ALA A 35 -165.60 -101.56 REMARK 500 10 SER A 4 -49.86 -153.45 REMARK 500 10 LEU A 5 -63.70 69.77 REMARK 500 10 TYR A 7 113.45 66.99 REMARK 500 10 ARG A 12 -62.97 -96.45 REMARK 500 10 HIS A 17 35.26 -154.28 REMARK 500 10 CYS A 34 -79.00 -129.20 REMARK 500 10 ALA A 35 -175.28 176.69 REMARK 500 11 SER A 4 27.43 175.60 REMARK 500 11 SER A 16 -1.84 67.57 REMARK 500 11 CYS A 34 -87.35 -130.06 REMARK 500 11 ALA A 35 -160.66 172.08 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16145 RELATED DB: BMRB REMARK 900 RELATED ID: 2KEC RELATED DB: PDB REMARK 900 RELATED ID: 2KED RELATED DB: PDB DBREF 2KEE A 1 68 UNP P48061 SDF1_HUMAN 22 89 SEQADV 2KEE GLY A -1 UNP P48061 EXPRESSION TAG SEQADV 2KEE SER A 0 UNP P48061 EXPRESSION TAG SEQRES 1 A 70 GLY SER 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 ALA A 19 ALA A 21 5 3 HELIX 2 2 LEU A 55 LYS A 68 1 14 SHEET 1 A 3 VAL A 23 ASN A 30 0 SHEET 2 A 3 LEU A 36 LEU A 42 -1 O ARG A 41 N LYS A 24 SHEET 3 A 3 GLN A 48 ILE A 51 -1 O ILE A 51 N ILE A 38 SSBOND 1 CYS A 9 CYS A 34 1555 1555 2.02 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 MODEL 1