HEADER LIGASE 21-NOV-11 2LM3 TITLE STRUCTURE OF THE RHESUS MONKEY TRIM5ALPHA PRYSPRY DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPARTITE MOTIF-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SPRY DOMAIN RESIDUES 292-497; COMPND 5 SYNONYM: TRIM5ALPHA; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 3 ORGANISM_COMMON: RHESUS MACAQUE,RHESUS MACAQUES,RHESUS MONKEYS; SOURCE 4 ORGANISM_TAXID: 9544; SOURCE 5 GENE: TRIM5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET 30A KEYWDS LIGASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.BIRIS,Y.YANG,A.B.TAYLOR,A.TOMASHEVSKI,M.GUO,P.J.HART,F.DIAZ- AUTHOR 2 GRIFFERO,D.N.IVANOV REVDAT 3 14-JUN-23 2LM3 1 REMARK SEQADV REVDAT 2 19-JUN-13 2LM3 1 JRNL REVDAT 1 08-AUG-12 2LM3 0 JRNL AUTH N.BIRIS,Y.YANG,A.B.TAYLOR,A.TOMASHEVSKI,M.GUO,P.J.HART, JRNL AUTH 2 F.DIAZ-GRIFFERO,D.N.IVANOV JRNL TITL STRUCTURE OF THE RHESUS MONKEY TRIM5ALPHA PRYSPRY DOMAIN, JRNL TITL 2 THE HIV CAPSID RECOGNITION MODULE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 13278 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22847415 JRNL DOI 10.1073/PNAS.1203536109 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE WHOLE PROTEIN WAS ASSIGNED BY NMR. REMARK 3 THE FINAL STRUCTURES OF THE PROTEIN WERE CALCULATED USING XPLOR- REMARK 3 NIH. SIMULATED ANNEALING WITH NOE-DERIVED DISTANCE RESTRAINTS REMARK 3 WAS APPLIED TO THE 325-349 LOOP ONLY WHEREAS RESIDUES 291-324 REMARK 3 WERE HELD FIXED AT THE COORDINATES DETERMINED BY X-RAY REMARK 3 CRYSTALLOGRAPHY FROM PDB ENTRY 3UV9. REMARK 4 REMARK 4 2LM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000102549. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 250 MM [U-98% 15N] SPRY, 93% REMARK 210 H2O/7% D2O; 250 MM [U-99% 13C; U- REMARK 210 99% 15N] SPRY, 93% H2O/7% D2O; REMARK 210 250 MM [U-13C; U-15N; U-2H] SPRY, REMARK 210 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 3D HN(COCA)CB; 3D 1H- REMARK 210 15N NOESY; 3D H(CCO)NH; 3D C(CO) REMARK 210 NH; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, NMRPIPE, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 290 REMARK 465 SER A 496 REMARK 465 SER A 497 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 ASP A 440 HG1 THR A 459 1.25 REMARK 500 HE21 GLN A 418 HH TYR A 466 1.33 REMARK 500 H ASP A 440 OG1 THR A 459 1.58 REMARK 500 O PHE A 340 HD22 ASN A 345 1.59 REMARK 500 HZ3 LYS A 372 O VAL A 488 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 ASN A 309 48.07 -108.10 REMARK 500 1 ARG A 325 -35.55 122.83 REMARK 500 1 ASN A 326 166.46 64.00 REMARK 500 1 PRO A 327 179.35 -41.71 REMARK 500 1 GLN A 328 -66.72 -17.11 REMARK 500 1 ILE A 329 49.04 -166.43 REMARK 500 1 TYR A 331 34.23 36.51 REMARK 500 1 ALA A 333 97.64 30.98 REMARK 500 1 PRO A 334 12.67 -67.64 REMARK 500 1 LEU A 337 -101.46 63.30 REMARK 500 1 THR A 339 -104.59 57.12 REMARK 500 1 PHE A 340 66.93 174.06 REMARK 500 1 PRO A 341 87.49 -39.43 REMARK 500 1 THR A 344 27.78 -179.93 REMARK 500 1 ASN A 345 -172.91 -41.78 REMARK 500 1 PHE A 346 18.83 53.90 REMARK 500 1 ASN A 347 129.00 -173.24 REMARK 500 1 CYS A 349 76.38 72.58 REMARK 500 1 SER A 360 161.76 168.48 REMARK 500 1 VAL A 369 51.77 -119.92 REMARK 500 1 ALA A 374 142.35 -174.35 REMARK 500 1 SER A 385 51.73 -109.19 REMARK 500 1 ASN A 390 61.50 19.54 REMARK 500 1 ILE A 391 -72.76 -66.34 REMARK 500 1 GLU A 395 46.01 35.43 REMARK 500 1 GLU A 410 -6.96 75.43 REMARK 500 1 PHE A 429 74.50 -105.77 REMARK 500 1 ASP A 447 72.57 -113.01 REMARK 500 1 CYS A 451 61.54 61.34 REMARK 500 1 ASN A 460 63.35 -109.44 REMARK 500 1 HIS A 461 14.34 53.66 REMARK 500 1 ARG A 484 64.16 69.97 REMARK 500 1 LYS A 485 -22.32 61.76 REMARK 500 1 CYS A 493 -114.94 -7.48 REMARK 500 1 SER A 494 102.28 114.83 REMARK 500 2 ASN A 309 47.45 -107.58 REMARK 500 2 ARG A 325 109.96 69.73 REMARK 500 2 PRO A 327 178.56 -45.77 REMARK 500 2 GLN A 328 -58.51 -23.89 REMARK 500 2 ILE A 329 44.48 -163.69 REMARK 500 2 TYR A 331 28.33 41.12 REMARK 500 2 ALA A 333 99.14 30.40 REMARK 500 2 PRO A 334 17.48 -69.74 REMARK 500 2 THR A 336 45.81 -106.20 REMARK 500 2 LEU A 337 -104.16 60.60 REMARK 500 2 THR A 339 -106.41 65.10 REMARK 500 2 PHE A 340 67.33 171.82 REMARK 500 2 PRO A 341 95.48 -34.81 REMARK 500 2 LEU A 343 -8.91 -50.32 REMARK 500 2 THR A 344 -33.60 -176.69 REMARK 500 REMARK 500 THIS ENTRY HAS 347 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18097 RELATED DB: BMRB REMARK 900 RELATED ID: 3UV9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PRIMATE INNATE IMMUNITY DBREF 2LM3 A 292 497 UNP Q0PF16 TRIM5_MACMU 292 497 SEQADV 2LM3 GLY A 290 UNP Q0PF16 EXPRESSION TAG SEQADV 2LM3 THR A 291 UNP Q0PF16 EXPRESSION TAG SEQADV 2LM3 THR A 307 UNP Q0PF16 PRO 307 VARIANT SEQRES 1 A 208 GLY THR GLU LEU THR ASP ALA ARG ARG TYR TRP VAL ASP SEQRES 2 A 208 VAL THR LEU ALA THR ASN ASN ILE SER HIS ALA VAL ILE SEQRES 3 A 208 ALA GLU ASP LYS ARG GLN VAL SER SER ARG ASN PRO GLN SEQRES 4 A 208 ILE MET TYR GLN ALA PRO GLY THR LEU PHE THR PHE PRO SEQRES 5 A 208 SER LEU THR ASN PHE ASN TYR CYS THR GLY VAL LEU GLY SEQRES 6 A 208 SER GLN SER ILE THR SER GLY LYS HIS TYR TRP GLU VAL SEQRES 7 A 208 ASP VAL SER LYS LYS SER ALA TRP ILE LEU GLY VAL CYS SEQRES 8 A 208 ALA GLY PHE GLN SER ASP ALA MET TYR ASN ILE GLU GLN SEQRES 9 A 208 ASN GLU ASN TYR GLN PRO LYS TYR GLY TYR TRP VAL ILE SEQRES 10 A 208 GLY LEU GLN GLU GLY VAL LYS TYR SER VAL PHE GLN ASP SEQRES 11 A 208 GLY SER SER HIS THR PRO PHE ALA PRO PHE ILE VAL PRO SEQRES 12 A 208 LEU SER VAL ILE ILE CYS PRO ASP ARG VAL GLY VAL PHE SEQRES 13 A 208 VAL ASP TYR GLU ALA CYS THR VAL SER PHE PHE ASN ILE SEQRES 14 A 208 THR ASN HIS GLY PHE LEU ILE TYR LYS PHE SER GLN CYS SEQRES 15 A 208 SER PHE SER LYS PRO VAL PHE PRO TYR LEU ASN PRO ARG SEQRES 16 A 208 LYS CYS THR VAL PRO MET THR LEU CYS SER PRO SER SER HELIX 1 1 THR A 291 ARG A 297 1 7 HELIX 2 2 ARG A 298 TRP A 300 5 3 HELIX 3 3 ILE A 391 GLU A 395 5 5 HELIX 4 4 GLN A 398 TYR A 401 5 4 SHEET 1 A 2 LEU A 305 ALA A 306 0 SHEET 2 A 2 LEU A 353 GLY A 354 -1 O LEU A 353 N ALA A 306 SHEET 1 B 3 VAL A 314 ILE A 315 0 SHEET 2 B 3 GLN A 321 SER A 323 -1 O SER A 323 N VAL A 314 SHEET 3 B 3 MET A 490 THR A 491 -1 O MET A 490 N VAL A 322 SHEET 1 C 4 LYS A 362 ASP A 368 0 SHEET 2 C 4 ARG A 441 ASP A 447 -1 O VAL A 444 N TRP A 365 SHEET 3 C 4 VAL A 453 ASN A 457 -1 O PHE A 456 N GLY A 443 SHEET 4 C 4 LEU A 464 PHE A 468 -1 O ILE A 465 N PHE A 455 SHEET 1 D 5 VAL A 431 PRO A 432 0 SHEET 2 D 5 LYS A 413 VAL A 416 -1 N VAL A 416 O VAL A 431 SHEET 3 D 5 TYR A 403 GLN A 409 -1 N GLY A 407 O SER A 415 SHEET 4 D 5 TRP A 375 CYS A 380 -1 N VAL A 379 O TRP A 404 SHEET 5 D 5 PHE A 478 ASN A 482 -1 O PHE A 478 N CYS A 380 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