HEADER VIRAL PROTEIN 21-JUL-10 2L0Z TITLE SOLUTION STRUCTURE OF A ZINC-BINDING DOMAIN FROM THE JUNIN VIRUS TITLE 2 ENVELOPE GLYCOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOPROTEIN G2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC-BINDING DOMAIN, UNP RESIDUES 445-485; COMPND 5 SYNONYM: GLYCOPROTEIN GPC, G2 SUBUNIT; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: JUNIN VIRUS; SOURCE 4 ORGANISM_COMMON: JUNV; SOURCE 5 ORGANISM_TAXID: 11619; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE, N-ACETYLATED KEYWDS ZINC-BINDING DOMAIN, VIRUS ENVELOPE GLYCOPROTEIN, GPC, JUNIN VIRUS, KEYWDS 2 ARENAVIRUS, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR K.BRIKNAROVA,J.YORK,J.H.NUNBERG REVDAT 2 26-JAN-11 2L0Z 1 JRNL REVDAT 1 10-NOV-10 2L0Z 0 JRNL AUTH K.BRIKNAROVA,C.J.THOMAS,J.YORK,J.H.NUNBERG JRNL TITL STRUCTURE OF A ZINC-BINDING DOMAIN IN THE JUNIN VIRUS JRNL TITL 2 ENVELOPE GLYCOPROTEIN. JRNL REF J.BIOL.CHEM. V. 286 1528 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21068387 JRNL DOI 10.1074/JBC.M110.166025 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN EXPLICIT SOLVENT (H2O) IN REMARK 3 ARIA REMARK 4 REMARK 4 2L0Z COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-10. REMARK 100 THE RCSB ID CODE IS RCSB101819. 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 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM JUNV ZBD PEPTIDE, 50 MM REMARK 210 [U-98% 2H] TRIS-2, 2.5 MM [U- REMARK 210 94.5% 2H] TCEP-3, 5 MM ZINC REMARK 210 SULFATE-4, 90% H2O/10% D2O; 0.7 REMARK 210 MM JUNV ZBD PEPTIDE, 50 MM [U-98% REMARK 210 2H] TRIS-6, 2.5 MM [U-94.5% 2H] REMARK 210 TCEP-7, 4 MM ZINC SULFATE-8, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY; 2D 1H-15N HSQC; 2D E REMARK 210 -COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 1.2, FELIX 2004 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 56 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 OE2 GLU A 453 H CYS A 455 1.76 REMARK 500 H HIS A 449 O VAL A 480 1.79 REMARK 500 OD1 ASN A 462 H LEU A 464 1.84 REMARK 500 H ASN A 462 O GLY A 466 1.91 REMARK 500 O HIS A 449 H VAL A 480 1.92 REMARK 500 O HIS A 447 H ARG A 482 1.98 REMARK 500 O LYS A 477 HG1 THR A 479 2.09 REMARK 500 HA LEU A 461 O GLY A 466 2.09 REMARK 500 H ILE A 450 OE1 GLU A 453 2.11 REMARK 500 O ASN A 462 H GLY A 465 2.11 REMARK 500 HE1 HIS A 447 OXT HIS A 485 2.13 REMARK 500 SG CYS A 467 HB3 LYS A 471 2.14 REMARK 500 O LEU A 464 H LYS A 476 2.19 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 14 ARG A 451 CD ARG A 451 NE 0.110 REMARK 500 20 HIS A 485 CB HIS A 485 CG -0.106 REMARK 500 21 TYR A 472 CE2 TYR A 472 CD2 0.091 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 11 ARG A 468 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 21 TYR A 472 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 21 TYR A 472 CG - CD2 - CE2 ANGL. DEV. = -6.3 DEGREES 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 ARG A 451 88.73 69.40 REMARK 500 1 CYS A 455 113.92 72.73 REMARK 500 1 LYS A 471 -44.76 -172.85 REMARK 500 1 LYS A 476 77.99 53.20 REMARK 500 1 PRO A 478 86.28 -60.46 REMARK 500 1 ARG A 483 13.47 -153.15 REMARK 500 2 ARG A 451 99.89 -62.18 REMARK 500 2 CYS A 455 117.59 173.35 REMARK 500 2 ASN A 462 -78.70 -59.59 REMARK 500 2 SER A 463 -30.58 -148.28 REMARK 500 2 LYS A 471 -80.45 -150.38 REMARK 500 2 PRO A 478 109.62 -55.81 REMARK 500 2 ARG A 483 -13.62 -145.17 REMARK 500 3 ARG A 451 100.05 -49.45 REMARK 500 3 ALA A 454 -78.13 -61.82 REMARK 500 3 SER A 463 -76.69 -174.87 REMARK 500 3 ARG A 468 -53.26 71.93 REMARK 500 3 LYS A 471 -74.83 106.94 REMARK 500 3 PRO A 473 -90.37 -83.03 REMARK 500 3 ASN A 474 -69.60 -125.33 REMARK 500 3 LEU A 475 -51.36 71.14 REMARK 500 3 LYS A 476 61.63 68.73 REMARK 500 4 ARG A 451 95.74 -60.04 REMARK 500 4 ALA A 454 -85.89 -68.68 REMARK 500 4 CYS A 469 -22.28 108.31 REMARK 500 4 LYS A 471 -61.28 -95.11 REMARK 500 4 ARG A 483 -64.54 -100.30 REMARK 500 5 ILE A 450 105.10 -59.80 REMARK 500 5 ARG A 451 17.73 56.42 REMARK 500 5 GLU A 453 -163.76 -78.24 REMARK 500 5 CYS A 455 106.58 170.32 REMARK 500 5 SER A 463 -66.45 -156.07 REMARK 500 5 LEU A 464 33.41 -83.09 REMARK 500 5 LYS A 471 -75.22 156.13 REMARK 500 5 PRO A 473 -164.64 -79.60 REMARK 500 5 PRO A 478 102.54 -29.67 REMARK 500 6 ARG A 451 92.35 73.38 REMARK 500 6 GLU A 453 -164.81 -127.95 REMARK 500 6 CYS A 455 118.08 71.75 REMARK 500 6 CYS A 469 141.92 84.22 REMARK 500 6 PRO A 478 99.91 -35.72 REMARK 500 6 ARG A 483 30.15 -142.46 REMARK 500 7 CYS A 455 106.96 179.60 REMARK 500 7 SER A 463 -71.44 -164.78 REMARK 500 7 LEU A 464 37.98 -85.50 REMARK 500 7 ARG A 468 88.83 -62.50 REMARK 500 7 CYS A 469 157.01 160.28 REMARK 500 7 LYS A 471 -56.97 -123.39 REMARK 500 7 PRO A 473 -178.83 -68.53 REMARK 500 7 PRO A 478 103.09 -41.93 REMARK 500 REMARK 500 THIS ENTRY HAS 139 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 486 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 449 NE2 REMARK 620 2 HIS A 485 NE2 110.6 REMARK 620 3 HIS A 447 NE2 108.5 109.2 REMARK 620 4 CYS A 455 SG 109.1 110.5 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 487 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 459 ND1 REMARK 620 2 CYS A 469 SG 109.0 REMARK 620 3 CYS A 467 SG 107.8 107.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 486 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 487 DBREF 2L0Z A 445 485 UNP P26313 GLYC_JUNIN 445 485 SEQADV 2L0Z ACE A 444 UNP P26313 ACETYLATION SEQRES 1 A 42 ACE PRO THR HIS ARG HIS ILE ARG GLY GLU ALA CYS PRO SEQRES 2 A 42 LEU PRO HIS ARG LEU ASN SER LEU GLY GLY CYS ARG CYS SEQRES 3 A 42 GLY LYS TYR PRO ASN LEU LYS LYS PRO THR VAL TRP ARG SEQRES 4 A 42 ARG GLY HIS HET ACE A 444 6 HET ZN A 486 1 HET ZN A 487 1 HETNAM ACE ACETYL GROUP HETNAM ZN ZINC ION FORMUL 1 ACE C2 H4 O FORMUL 2 ZN 2(ZN 2+) SHEET 1 A 2 HIS A 447 HIS A 449 0 SHEET 2 A 2 VAL A 480 ARG A 482 -1 O VAL A 480 N HIS A 449 LINK NE2 HIS A 449 ZN ZN A 486 1555 1555 2.09 LINK NE2 HIS A 485 ZN ZN A 486 1555 1555 2.09 LINK NE2 HIS A 447 ZN ZN A 486 1555 1555 2.10 LINK ND1 HIS A 459 ZN ZN A 487 1555 1555 2.12 LINK SG CYS A 455 ZN ZN A 486 1555 1555 2.30 LINK SG CYS A 469 ZN ZN A 487 1555 1555 2.31 LINK SG CYS A 467 ZN ZN A 487 1555 1555 2.32 CISPEP 1 LEU A 457 PRO A 458 1 2.24 CISPEP 2 LEU A 457 PRO A 458 2 4.02 CISPEP 3 LEU A 457 PRO A 458 3 4.74 CISPEP 4 LEU A 457 PRO A 458 4 5.62 CISPEP 5 LEU A 457 PRO A 458 5 7.49 CISPEP 6 LEU A 457 PRO A 458 6 5.53 CISPEP 7 LEU A 457 PRO A 458 7 4.65 CISPEP 8 LEU A 457 PRO A 458 8 8.25 CISPEP 9 LEU A 457 PRO A 458 9 3.55 CISPEP 10 LEU A 457 PRO A 458 10 6.31 CISPEP 11 LEU A 457 PRO A 458 11 4.94 CISPEP 12 LEU A 457 PRO A 458 12 7.75 CISPEP 13 LEU A 457 PRO A 458 13 6.56 CISPEP 14 LEU A 457 PRO A 458 14 1.92 CISPEP 15 LEU A 457 PRO A 458 15 2.63 CISPEP 16 LEU A 457 PRO A 458 16 3.92 CISPEP 17 LEU A 457 PRO A 458 17 6.27 CISPEP 18 LEU A 457 PRO A 458 18 3.40 CISPEP 19 LEU A 457 PRO A 458 19 5.94 CISPEP 20 LEU A 457 PRO A 458 20 5.24 CISPEP 21 LEU A 457 PRO A 458 21 5.04 SITE 1 AC1 4 HIS A 447 HIS A 449 CYS A 455 HIS A 485 SITE 1 AC2 3 HIS A 459 CYS A 467 CYS A 469 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 HETATM 1 C ACE A 444 -5.743 -8.469 -4.325 1.00 0.00 C HETATM 2 O ACE A 444 -5.007 -9.342 -4.787 1.00 0.00 O HETATM 3 CH3 ACE A 444 -7.052 -8.837 -3.653 1.00 0.00 C HETATM 4 H1 ACE A 444 -7.747 -9.208 -4.392 1.00 0.00 H HETATM 5 H2 ACE A 444 -7.468 -7.963 -3.174 1.00 0.00 H HETATM 6 H3 ACE A 444 -6.872 -9.600 -2.912 1.00 0.00 H