PDB Short entry for 2K01 HEADER CYTOKINE 23-JAN-08 2K01 TITLE STRUCTURE OF A LOCKED SDF1 DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMAL CELL-DERIVED FACTOR 1; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: SDF-1-ALPHA(3-67) DOMAIN; COMPND 5 SYNONYM: SDF-1, C-X-C MOTIF CHEMOKINE 12, PRE-B CELL GROWTH- COMPND 6 STIMULATING FACTOR, PBSF, HIRH; COMPND 7 ENGINEERED: YES; COMPND 8 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_STRAIN: SG130099[PREP4]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PQE30-6HT KEYWDS STROMAL CELL DERIVED FACTOR-1, SDF1-ALPHA, CXCL12, CHEMOKINE, KEYWDS 2 SULFOTYROSINE, LOCKED DIMER, ALTERNATIVE SPLICING, CHEMOTAXIS, KEYWDS 3 CYTOKINE, GROWTH FACTOR, SECRETED EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.F.VOLKMAN,C.T.VELDKAMP,F.C.PETERSON REVDAT 6 14-JUN-23 2K01 1 REMARK REVDAT 5 20-OCT-21 2K01 1 SEQADV REVDAT 4 19-FEB-20 2K01 1 REMARK SEQADV REVDAT 3 24-FEB-09 2K01 1 VERSN REVDAT 2 04-NOV-08 2K01 1 JRNL REVDAT 1 28-OCT-08 2K01 0 JRNL AUTH C.T.VELDKAMP,C.SEIBERT,F.C.PETERSON,N.B.DE LA CRUZ, JRNL AUTH 2 J.C.HAUGNER,H.BASNET,T.P.SAKMAR,B.F.VOLKMAN JRNL TITL STRUCTURAL BASIS OF CXCR4 SULFOTYROSINE RECOGNITION BY THE JRNL TITL 2 CHEMOKINE SDF-1/CXCL12 JRNL REF SCI.SIGNAL. V. 1 RA4 2008 JRNL REFN ESSN 1937-9145 JRNL PMID 18799424 JRNL DOI 10.1126/SCISIGNAL.1160755 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.3 REMARK 3 AUTHORS : REMARK 3 SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CXCL12 DIMER STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 REMARK 3 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS REMARK 3 (CXCL12 TO CXCL12), AND 138 PHI AND PSI DIHEDRAL ANGLE REMARK 3 CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN REMARK 3 ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A REMARK 3 SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT REMARK 3 TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS., REMARK 3 CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE REMARK 3 CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG REMARK 3 RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12) REMARK 3 , AND 138 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT REMARK 3 WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX REMARK 3 AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN REMARK 3 THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE REMARK 3 CONSTRAINTS FROM BOTH MONOMERS. REMARK 4 REMARK 4 2K01 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000100504. 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 : 21 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.620 MM [U-100% 13C; U-100% REMARK 210 15N] CXCL12/SDF1-ALPHA, 90% H2O, REMARK 210 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 : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, NMRPIPE 2004, XEASY REMARK 210 1.3, SPSCAN 1.1.0, GARANT 2.1, REMARK 210 CYANA 2.1 REMARK 210 METHOD USED : AUTOMATED METHODS WERE USED FOR REMARK 210 BACKBONE CHEMICAL SHIFT REMARK 210 ASSIGNMENT AND ITERATIVE NOE REMARK 210 REFINEMENT. FINAL STRUCTURES REMARK 210 WERE OBTAINED BY MOLECULAR REMARK 210 DYNAMICS IN EXPLICIT SOLVENT, REMARK 210 AUTOMATED METHODS WERE USED FOR REMARK 210 BACKBONE CHEMICAL SHIFT REMARK 210 ASSIGNMENT AND ITERATIVE NOE REMARK 210 REFINEMENT. FINAL STRUCTURES REMARK 210 WERE OBTAINED BY MOLECULAR REMARK 210 DYNAMICS IN EXPLICIT SOLVENT 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, C 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 MET A 0 REMARK 465 GLY C 199 REMARK 465 MET C 200 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 TYR A 7 -53.43 75.28 REMARK 500 1 CYS A 36 108.18 -50.32 REMARK 500 1 ASN A 44 -76.39 49.23 REMARK 500 1 ARG A 47 -167.30 -103.44 REMARK 500 1 ASN A 67 -3.39 62.21 REMARK 500 1 TYR C 207 -57.17 74.65 REMARK 500 1 CYS C 236 119.09 72.05 REMARK 500 1 ASN C 244 -84.83 53.52 REMARK 500 1 ARG C 247 -162.07 -111.65 REMARK 500 1 ASN C 267 78.74 43.86 REMARK 500 2 SER A 6 -165.35 66.59 REMARK 500 2 ARG A 12 -50.02 -125.78 REMARK 500 2 HIS A 17 46.21 -83.40 REMARK 500 2 CYS A 36 99.61 -63.68 REMARK 500 2 ASN A 44 -177.86 162.77 REMARK 500 2 ASN A 46 -167.84 -129.30 REMARK 500 2 SER C 206 -151.31 61.36 REMARK 500 2 ARG C 212 -50.86 -125.10 REMARK 500 2 CYS C 236 106.60 65.02 REMARK 500 2 ASN C 244 -83.52 71.98 REMARK 500 2 ASN C 245 85.72 -163.36 REMARK 500 2 ASN C 267 78.11 42.34 REMARK 500 3 SER A 6 40.95 -169.02 REMARK 500 3 TYR A 7 -34.56 72.72 REMARK 500 3 ASN A 44 -77.80 172.48 REMARK 500 3 ASN A 45 21.89 -162.91 REMARK 500 3 ASN A 67 -57.33 70.65 REMARK 500 3 TYR C 207 -9.11 80.95 REMARK 500 3 HIS C 217 34.04 -83.92 REMARK 500 3 ASN C 244 -89.06 167.94 REMARK 500 3 ASN C 245 74.90 -151.13 REMARK 500 4 TYR A 7 -48.34 70.67 REMARK 500 4 ASN A 44 30.98 -77.99 REMARK 500 4 ASN A 67 -34.18 64.62 REMARK 500 4 TYR C 207 -39.53 68.78 REMARK 500 4 ASN C 233 79.27 -159.31 REMARK 500 4 CYS C 236 103.76 61.86 REMARK 500 4 ARG C 247 -165.18 -113.72 REMARK 500 5 PRO A 2 97.61 -55.28 REMARK 500 5 VAL A 3 139.76 178.55 REMARK 500 5 SER A 4 118.66 -164.33 REMARK 500 5 LEU A 5 90.84 -69.30 REMARK 500 5 TYR A 7 48.23 -86.29 REMARK 500 5 CYS A 36 103.73 -58.52 REMARK 500 5 ASN A 44 -161.52 68.11 REMARK 500 5 ASN C 244 -99.64 53.65 REMARK 500 6 VAL A 3 99.97 72.08 REMARK 500 6 SER A 6 -168.52 -171.76 REMARK 500 6 PRO A 10 -71.12 -37.75 REMARK 500 6 CYS A 36 101.64 71.77 REMARK 500 REMARK 500 THIS ENTRY HAS 197 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15633 RELATED DB: BMRB DBREF 2K01 A 1 68 UNP P48061 SDF1_HUMAN 22 89 DBREF 2K01 C 201 268 UNP P48061 SDF1_HUMAN 22 89 SEQADV 2K01 GLY A -1 UNP P48061 EXPRESSION TAG SEQADV 2K01 MET A 0 UNP P48061 EXPRESSION TAG SEQADV 2K01 CYS A 36 UNP P48061 LEU 57 ENGINEERED MUTATION SEQADV 2K01 CYS A 65 UNP P48061 ALA 86 ENGINEERED MUTATION SEQADV 2K01 GLY C 199 UNP P48061 EXPRESSION TAG SEQADV 2K01 MET C 200 UNP P48061 EXPRESSION TAG SEQADV 2K01 CYS C 236 UNP P48061 LEU 57 ENGINEERED MUTATION SEQADV 2K01 CYS C 265 UNP P48061 ALA 86 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 CYS 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 CYS LEU ASN LYS SEQRES 1 C 70 GLY MET LYS PRO VAL SER LEU SER TYR ARG CYS PRO CYS SEQRES 2 C 70 ARG PHE PHE GLU SER HIS VAL ALA ARG ALA ASN VAL LYS SEQRES 3 C 70 HIS LEU LYS ILE LEU ASN THR PRO ASN CYS ALA CYS GLN SEQRES 4 C 70 ILE VAL ALA ARG LEU LYS ASN ASN ASN ARG GLN VAL CYS SEQRES 5 C 70 ILE ASP PRO LYS LEU LYS TRP ILE GLN GLU TYR LEU GLU SEQRES 6 C 70 LYS CYS LEU ASN LYS HELIX 1 1 LEU A 55 LYS A 64 1 10 HELIX 2 2 LEU C 255 LYS C 264 1 10 SHEET 1 A 6 GLN A 48 ILE A 51 0 SHEET 2 A 6 GLN A 37 LEU A 42 -1 N ALA A 40 O VAL A 49 SHEET 3 A 6 VAL A 23 LEU A 29 -1 N LYS A 24 O ARG A 41 SHEET 4 A 6 VAL C 223 LEU C 229 -1 O ILE C 228 N LEU A 26 SHEET 5 A 6 GLN C 237 LEU C 242 -1 O ARG C 241 N LYS C 224 SHEET 6 A 6 GLN C 248 ILE C 251 -1 O ILE C 251 N ILE C 238 SSBOND 1 CYS A 9 CYS A 34 1555 1555 2.04 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.01 SSBOND 3 CYS A 36 CYS C 265 1555 1555 2.04 SSBOND 4 CYS A 65 CYS C 236 1555 1555 2.03 SSBOND 5 CYS C 209 CYS C 234 1555 1555 2.04 SSBOND 6 CYS C 211 CYS C 250 1555 1555 2.01 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