HEADER CYTOKINE 24-JAN-08 2K04 TITLE STRUCTURE OF SDF1 IN COMPLEX WITH THE CXCR4 N-TERMINUS CONTAINING NO TITLE 2 SULFOTYROSINES 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; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: C-X-C CHEMOKINE RECEPTOR TYPE 4; COMPND 11 CHAIN: B, D; COMPND 12 FRAGMENT: N-TERMINUS, RESIDUES 1-38; COMPND 13 SYNONYM: CXC-R4, CXCR-4, STROMAL CELL- DERIVED FACTOR 1 RECEPTOR, COMPND 14 SDF-1 RECEPTOR, FUSIN, LEUKOCYTE-DERIVED SEVEN TRANSMEMBRANE DOMAIN COMPND 15 RECEPTOR, LESTR, LCR1, FB22, NPYRL, HM89, CD184 ANTIGEN; 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_STRAIN: SD13009[PREP4]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PQE30-6HT; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CXCR4; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: SD13009[PREP4]; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PQE30-GB1 KEYWDS STROMAL CELL DERIVED FACTOR-1, SDF1-ALPHA, CXCL12, CXCR4, CHEMOKINE, KEYWDS 2 LOCKED DIMER, ALTERNATIVE SPLICING, CHEMOTAXIS, CYTOKINE, GROWTH KEYWDS 3 FACTOR, SECRETED, G-PROTEIN COUPLED RECEPTOR, GLYCOPROTEIN, HOST- KEYWDS 4 VIRUS INTERACTION, MEMBRANE, RECEPTOR, SULFATION, TRANSDUCER, KEYWDS 5 TRANSMEMBRANE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.F.VOLKMAN,C.T.VELDKAMP,F.C.PETERSON REVDAT 7 14-JUN-23 2K04 1 REMARK REVDAT 6 20-OCT-21 2K04 1 SEQADV REVDAT 5 19-FEB-20 2K04 1 REMARK SEQADV REVDAT 4 22-NOV-17 2K04 1 REMARK REVDAT 3 24-FEB-09 2K04 1 VERSN REVDAT 2 04-NOV-08 2K04 1 JRNL REVDAT 1 28-OCT-08 2K04 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/CXCR4 COMPLEX STRUCTURES ARE REMARK 3 BASED ON A TOTAL OF 2012 NOE CONSTRAINTS ( 744 INTRA, 384 REMARK 3 SEQUENTIAL, 238 MEDIUM, 444 LONG RANGE, 110 CXCL12 INTERMONOMER REMARK 3 CONSTRAINTS (CXCL12 TO CXCL12), AND 92 INTERMOLECULAR REMARK 3 CONSTRAINTS (CXCL12 TO CXCR4)) AND 128 PHI AND PSI DIHEDRAL REMARK 3 ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED REMARK 3 IN 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 4 REMARK 4 2K04 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000100507. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 21 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : .31 MM [U-100% 13C; U-100% 15N] REMARK 210 CXCL12/SDF1-ALPHA, .775 MM CXCR4, REMARK 210 90% H2O/10% D2O; 1.0 MM [U-100% REMARK 210 13C; U-100% 15N] CXCR4, 0.625 MM REMARK 210 CXCL12/SDF1-ALPHA, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C-SEPARATED_NOESY (AROMATIC); 3D_13C-F1- REMARK 210 FILTERED_13C-F3-SEPARATEDED_NOESY 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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 B 99 REMARK 465 SER B 100 REMARK 465 GLY C 199 REMARK 465 MET C 200 REMARK 465 GLY D 299 REMARK 465 SER D 300 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 OD2 ASP B 110 HD1 HIS C 225 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 5 TYR B 112 CE2 TYR B 112 CD2 -0.091 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 ALA A 35 -169.46 -66.23 REMARK 500 1 ASN A 44 94.39 -67.95 REMARK 500 1 ASN A 45 -40.33 172.14 REMARK 500 1 ARG A 47 -82.91 -128.08 REMARK 500 1 PRO A 53 30.49 -85.24 REMARK 500 1 ASN A 67 98.04 -167.02 REMARK 500 1 SER B 109 89.36 66.20 REMARK 500 1 ASN B 111 77.05 65.00 REMARK 500 1 MET B 116 117.15 75.84 REMARK 500 1 SER B 118 -174.20 71.09 REMARK 500 1 ASP B 120 136.85 74.16 REMARK 500 1 TYR B 121 -69.73 -105.45 REMARK 500 1 SER B 123 -152.68 60.00 REMARK 500 1 PHE B 129 -57.75 69.26 REMARK 500 1 SER C 206 -166.10 -163.27 REMARK 500 1 HIS C 217 -88.71 80.61 REMARK 500 1 VAL C 218 166.22 62.02 REMARK 500 1 PRO C 232 28.63 -63.95 REMARK 500 1 ASN C 233 23.50 -164.26 REMARK 500 1 CYS C 236 93.50 -62.94 REMARK 500 1 ASN C 245 -52.65 -172.08 REMARK 500 1 ASN C 246 -72.38 -152.65 REMARK 500 1 ARG C 247 -150.40 -169.54 REMARK 500 1 SER D 305 166.86 179.34 REMARK 500 1 ILE D 306 -157.32 -104.94 REMARK 500 1 SER D 318 175.72 69.09 REMARK 500 1 ASP D 320 160.11 72.29 REMARK 500 1 TYR D 321 -73.92 -129.61 REMARK 500 1 ASP D 322 -155.66 -145.07 REMARK 500 1 ALA D 334 -46.53 -163.00 REMARK 500 2 PRO A 2 39.07 -98.34 REMARK 500 2 VAL A 3 91.78 63.63 REMARK 500 2 LEU A 5 87.07 -165.75 REMARK 500 2 HIS A 25 168.90 179.96 REMARK 500 2 PRO A 32 16.19 -62.35 REMARK 500 2 ASN A 33 14.59 -153.05 REMARK 500 2 LYS A 43 40.16 -68.84 REMARK 500 2 ASN A 44 159.13 69.77 REMARK 500 2 ASN A 45 -45.62 71.62 REMARK 500 2 ASN A 67 -70.02 -88.32 REMARK 500 2 ILE B 106 -176.19 -68.56 REMARK 500 2 THR B 108 86.66 74.37 REMARK 500 2 THR B 113 82.47 -55.24 REMARK 500 2 ASP B 120 118.36 -166.07 REMARK 500 2 TYR B 121 -44.62 -161.18 REMARK 500 2 ASP B 122 -175.39 -175.36 REMARK 500 2 MET B 124 141.59 171.71 REMARK 500 2 GLU B 126 144.03 77.81 REMARK 500 2 GLU B 131 143.18 66.33 REMARK 500 2 PHE B 136 -74.03 -103.77 REMARK 500 REMARK 500 THIS ENTRY HAS 555 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 15 ARG C 220 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K01 RELATED DB: PDB REMARK 900 RELATED ID: 2K03 RELATED DB: PDB REMARK 900 RELATED ID: 2K05 RELATED DB: PDB REMARK 900 RELATED ID: 15636 RELATED DB: BMRB DBREF 2K04 A 1 68 UNP P48061 SDF1_HUMAN 22 89 DBREF 2K04 B 101 138 UNP P61073 CXCR4_HUMAN 1 38 DBREF 2K04 C 201 268 UNP P48061 SDF1_HUMAN 22 89 DBREF 2K04 D 301 338 UNP P61073 CXCR4_HUMAN 1 38 SEQADV 2K04 GLY A -1 UNP P48061 EXPRESSION TAG SEQADV 2K04 MET A 0 UNP P48061 EXPRESSION TAG SEQADV 2K04 CYS A 36 UNP P48061 LEU 57 ENGINEERED MUTATION SEQADV 2K04 CYS A 65 UNP P48061 ALA 86 ENGINEERED MUTATION SEQADV 2K04 GLY B 99 UNP P61073 EXPRESSION TAG SEQADV 2K04 SER B 100 UNP P61073 EXPRESSION TAG SEQADV 2K04 ALA B 128 UNP P61073 CYS 28 ENGINEERED MUTATION SEQADV 2K04 GLY C 199 UNP P48061 EXPRESSION TAG SEQADV 2K04 MET C 200 UNP P48061 EXPRESSION TAG SEQADV 2K04 CYS C 236 UNP P48061 LEU 57 ENGINEERED MUTATION SEQADV 2K04 CYS C 265 UNP P48061 ALA 86 ENGINEERED MUTATION SEQADV 2K04 GLY D 299 UNP P61073 EXPRESSION TAG SEQADV 2K04 SER D 300 UNP P61073 EXPRESSION TAG SEQADV 2K04 ALA D 328 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 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 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 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 SEQRES 1 D 40 GLY SER MET GLU GLY ILE SER ILE TYR THR SER ASP ASN SEQRES 2 D 40 TYR THR GLU GLU MET GLY SER GLY ASP TYR ASP SER MET SEQRES 3 D 40 LYS GLU PRO ALA PHE ARG GLU GLU ASN ALA ASN PHE ASN SEQRES 4 D 40 LYS HELIX 1 1 ALA A 19 ALA A 21 5 3 HELIX 2 2 LEU A 55 LEU A 66 1 12 HELIX 3 3 LEU C 255 LEU C 266 1 12 SHEET 1 A 6 GLN A 48 ILE A 51 0 SHEET 2 A 6 ILE A 38 LEU A 42 -1 N ILE A 38 O ILE A 51 SHEET 3 A 6 VAL A 23 ILE A 28 -1 N LYS A 27 O VAL A 39 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 2.01 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 2.04 SSBOND 5 CYS C 209 CYS C 234 1555 1555 2.03 SSBOND 6 CYS C 211 CYS C 250 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