HEADER IMMUNE SYSTEM 09-FEB-11 2L9H TITLE OLIGOMERIC STRUCTURE OF THE CHEMOKINE CCL5/RANTES FROM NMR, MS, AND TITLE 2 SAXS DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-C MOTIF CHEMOKINE 5; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: EOCP, EOSINOPHIL CHEMOTACTIC CYTOKINE, SIS-DELTA, SMALL- COMPND 5 INDUCIBLE CYTOKINE A5, T CELL-SPECIFIC PROTEIN P228, TCP228, T-CELL- COMPND 6 SPECIFIC PROTEIN RANTES; COMPND 7 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: CCL5, D17S136E, SCYA5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-23 KEYWDS IMMUNE SYSTEM, CHEMOKINE, OLIGOMER EXPDTA SOLUTION NMR; SOLUTION SCATTERING AUTHOR X.WANG,C.M.WATSON,J.S.SHARP,T.M.HANDEL,J.H.PRESTEGARD REVDAT 2 24-AUG-11 2L9H 1 JRNL VERSN REVDAT 1 22-JUN-11 2L9H 0 JRNL AUTH X.WANG,C.WATSON,J.S.SHARP,T.M.HANDEL,J.H.PRESTEGARD JRNL TITL OLIGOMERIC STRUCTURE OF THE CHEMOKINE CCL5/RANTES FROM NMR, JRNL TITL 2 MS, AND SAXS DATA. JRNL REF STRUCTURE V. 19 1138 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21827949 JRNL DOI 10.1016/J.STR.2011.06.001 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NAMD, VMD REMARK 3 AUTHORS : PHILLIPS, BRAUN, WANG, GUMBART, TAJKHORSHID, REMARK 3 VILLA, CHIPOT, SKEEL, KALE, AND SCHULTE (NAMD), REMARK 3 HUMPHREY, DALKE & SCHULTEN. (VMD) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-11. REMARK 100 THE RCSB ID CODE IS RCSB102124. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 297 REMARK 210 PH : 4.4 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] CCL5, 50 MM REMARK 210 SODIUM ACETATE, 90% H2O/10% D2O; REMARK 210 1 MM [U-100% 15N] CCL5, 50 MM REMARK 210 SODIUM ACETATE, 5 % REMARK 210 POLYACRYLAMIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N J-MOD TROSY; 2D 1H-15N REMARK 210 TROSY; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, VNMRJ REMARK 210 METHOD USED : MOLECULAR DYNAMICS, SAXS- REMARK 210 POTENTIAL GUIDED SCORING WITHIN REMARK 210 GRID SEARCH REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION BASED ON SAXS & REMARK 210 KNOWLEDGE-BASED POTENTIAL 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 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : BRUKER NANOSTARU TXS REMARK 265 SYNCHROTRON (Y/N) : N REMARK 265 BEAMLINE TYPE : NULL REMARK 265 BEAMLINE INSTRUMENT : BRUKER NANOSTARU REMARK 265 DETECTOR TYPE : AXS VANTEC 2000 REMARK 265 DETECTOR MANUFACTURER DETAILS : BRUKER REMARK 265 TEMPERATURE (KELVIN) : 288 REMARK 265 PH : 4.5 REMARK 265 NUMBER OF TIME FRAMES USED : 10 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 7 - 10 REMARK 265 SAMPLE BUFFER : ACETATE REMARK 265 DATA REDUCTION SOFTWARE : SAXS FOR WINDOWS XP REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 31 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.01 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 121 REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: CONSTRAINED SCATTERING REMARK 265 FITTING INCORPORATING NMR REMARK 265 RDC DATA. REMARK 265 SOFTWARE USED : VMD, GNOM, OLIGOMER REMARK 265 SOFTWARE AUTHORS : UIUC, EMBL REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : 5953 REMARK 265 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 265 CONFORMERS, SELECTION CRITERIA : THE MODELS WERE GENERATED USING REMARK 265 GRID SEARCH, CONTRAINING THE ORIENTATION BETWEEN THE DIMERS REMARK 265 ACCORDING TO NMR RDC DATA. MODELS WERE THEN SCORED BASED ON REMARK 265 AGREEMENT BETWEEN THEORETICAL AND EXPERIMENTAL SCATTERING CURVE REMARK 265 AND SOUNDNESS OF THE INTERFACE AS DEFINED BY A RESIDUE PAIRING REMARK 265 SCORE. REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 265 REMARK 265 OTHER DETAILS: PDB CODE 1U4L 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 RES C SSSEQI REMARK 465 SER A 1 REMARK 465 SER B 1 REMARK 465 PRO B 2 REMARK 465 TYR B 3 REMARK 465 SER C 1 REMARK 465 SER D 1 REMARK 465 PRO D 2 REMARK 465 TYR D 3 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 OD1 ASP A 6 HH21 ARG B 47 1.55 REMARK 500 HZ2 LYS B 25 OE1 GLU B 26 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 LEU A 65 CB - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 PHE C 28 CB - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 VAL C 42 CB - CA - C ANGL. DEV. = 12.5 DEGREES 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 PHE A 41 0.07 SIDE CHAIN REMARK 500 ARG A 59 0.14 SIDE CHAIN REMARK 500 ARG B 59 0.12 SIDE CHAIN REMARK 500 TYR C 3 0.07 SIDE CHAIN REMARK 500 TYR C 27 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 46 23.7 L L OUTSIDE RANGE REMARK 500 LEU A 65 2.8 L L EXPECTING SP3 REMARK 500 ASN B 46 25.0 L L OUTSIDE RANGE REMARK 500 PHE C 28 21.7 L L OUTSIDE RANGE REMARK 500 GLU C 66 21.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U4L RELATED DB: PDB REMARK 900 OLIGOMER STRUCTURE BASED ON THE DIMER REMARK 900 RELATED ID: 17453 RELATED DB: BMRB DBREF 2L9H A 1 68 UNP P13501 CCL5_HUMAN 24 91 DBREF 2L9H B 1 68 UNP P13501 CCL5_HUMAN 24 91 DBREF 2L9H C 1 68 UNP P13501 CCL5_HUMAN 24 91 DBREF 2L9H D 1 68 UNP P13501 CCL5_HUMAN 24 91 SEQRES 1 A 68 SER PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 A 68 TYR ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU SEQRES 3 A 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 A 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 A 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 A 68 GLU MET SER SEQRES 1 B 68 SER PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 B 68 TYR ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU SEQRES 3 B 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 B 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 B 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 B 68 GLU MET SER SEQRES 1 C 68 SER PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 C 68 TYR ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU SEQRES 3 C 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 C 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 C 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 C 68 GLU MET SER SEQRES 1 D 68 SER PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 D 68 TYR ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU SEQRES 3 D 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 D 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 D 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 D 68 GLU MET SER HELIX 1 1 PRO A 20 ALA A 22 5 3 HELIX 2 2 LYS A 55 GLU A 66 1 12 HELIX 3 3 PRO B 20 ALA B 22 5 3 HELIX 4 4 LYS B 55 SER B 68 1 14 HELIX 5 5 PRO C 20 ALA C 22 5 3 HELIX 6 6 LYS C 55 GLU C 66 1 12 HELIX 7 7 PRO D 20 ALA D 22 5 3 HELIX 8 8 LYS D 55 SER D 68 1 14 SHEET 1 A 2 THR A 8 CYS A 10 0 SHEET 2 A 2 THR B 8 CYS B 10 -1 O CYS B 10 N THR A 8 SHEET 1 B 3 ILE A 24 TYR A 29 0 SHEET 2 B 3 VAL A 39 THR A 43 -1 O VAL A 42 N GLU A 26 SHEET 3 B 3 GLN A 48 ALA A 51 -1 O ALA A 51 N VAL A 39 SHEET 1 C 3 ILE B 24 TYR B 29 0 SHEET 2 C 3 VAL B 39 THR B 43 -1 O VAL B 40 N PHE B 28 SHEET 3 C 3 GLN B 48 ALA B 51 -1 O VAL B 49 N PHE B 41 SHEET 1 D 2 THR C 8 CYS C 10 0 SHEET 2 D 2 THR D 8 CYS D 10 -1 O CYS D 10 N THR C 8 SHEET 1 E 3 ILE C 24 TYR C 29 0 SHEET 2 E 3 VAL C 39 THR C 43 -1 O VAL C 42 N GLU C 26 SHEET 3 E 3 GLN C 48 ALA C 51 -1 O ALA C 51 N VAL C 39 SHEET 1 F 3 ILE D 24 TYR D 29 0 SHEET 2 F 3 VAL D 39 THR D 43 -1 O VAL D 40 N PHE D 28 SHEET 3 F 3 GLN D 48 ALA D 51 -1 O VAL D 49 N PHE D 41 SSBOND 1 CYS A 11 CYS A 50 1555 1555 2.03 SSBOND 2 CYS B 11 CYS B 50 1555 1555 2.03 SSBOND 3 CYS C 11 CYS C 50 1555 1555 2.03 SSBOND 4 CYS D 11 CYS D 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