HEADER PROTEIN TRANSPORT/VIRAL PROTEIN 21-DEC-12 3ZHF TITLE GAMMA 2 ADAPTIN EAR DOMAIN CRYSTAL STRUCTURE WITH PRES1 SITE1 PEPTIDE TITLE 2 NPDWDFN CAVEAT 3ZHF CHAIN B LOW AFFINITY MEANS LOW CONFIDENCE IN MODEL. RESIDUES CAVEAT 2 3ZHF PHE B6 AND TRP B4 WERE REMODELLED MORE CONFIDENTLY THAN CAVEAT 3 3ZHF OTHER RESIDUES IN CHAIN B. COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EAR DOMAIN, RESIDUES 665-785; COMPND 5 SYNONYM: GAMMA2-ADAPTIN, G2AD; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LARGE ENVELOPE PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: PRES1 DOMAIN, RESIDUES 85-91; COMPND 11 SYNONYM: HBV L PROTEIN; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: AMIDATED C-TERMINUS, CARBOXYLATED N-TERMINUS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: MODIFIED PRSETA; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HEPATITIS B VIRUS; SOURCE 13 ORGANISM_TAXID: 10407 KEYWDS PROTEIN TRANSPORT-VIRAL PROTEIN COMPLEX, GAE EXPDTA X-RAY DIFFRACTION AUTHOR M.C.JUERGENS,J.VOROS,G.RAUTUREAU,D.SHEPHERD,V.E.PYE,J.MULDOON, AUTHOR 2 C.M.JOHNSON,A.ASHCROFT,S.M.V.FREUND,N.FERGUSON REVDAT 10 20-NOV-24 3ZHF 1 REMARK REVDAT 9 20-DEC-23 3ZHF 1 REMARK LINK REVDAT 8 23-OCT-19 3ZHF 1 SEQADV LINK REVDAT 7 07-MAR-18 3ZHF 1 SOURCE REMARK REVDAT 6 01-JUL-15 3ZHF 1 REMARK REVDAT 5 28-AUG-13 3ZHF 1 JRNL REVDAT 4 31-JUL-13 3ZHF 1 SOURCE REVDAT 3 24-JUL-13 3ZHF 1 JRNL REVDAT 2 17-JUL-13 3ZHF 1 SOURCE JRNL REVDAT 1 10-JUL-13 3ZHF 0 JRNL AUTH M.C.JURGENS,J.VOROS,G.J.P.RAUTUREAU,D.A.SHEPHERD,V.E.PYE, JRNL AUTH 2 J.MULDOON,C.M.JOHNSON,A.E.ASHCROFT,S.M.V.FREUND,N.FERGUSON JRNL TITL THE HEPATITIS B VIRUS PRES1 DOMAIN HIJACKS HOST TRAFFICKING JRNL TITL 2 PROTEINS BY MOTIF MIMICRY. JRNL REF NAT.CHEM.BIOL. V. 9 540 2013 JRNL REFN ISSN 1552-4450 JRNL PMID 23851574 JRNL DOI 10.1038/NCHEMBIO.1294 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 15598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.3052 - 3.0886 0.98 2613 122 0.1886 0.2061 REMARK 3 2 3.0886 - 2.4517 0.99 2495 133 0.1944 0.2240 REMARK 3 3 2.4517 - 2.1418 0.98 2445 133 0.1780 0.2612 REMARK 3 4 2.1418 - 1.9460 0.99 2422 135 0.1739 0.2186 REMARK 3 5 1.9460 - 1.8065 0.98 2418 133 0.1918 0.2502 REMARK 3 6 1.8065 - 1.7000 0.99 2426 123 0.2398 0.2697 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1115 REMARK 3 ANGLE : 1.081 1527 REMARK 3 CHIRALITY : 0.072 170 REMARK 3 PLANARITY : 0.005 204 REMARK 3 DIHEDRAL : 14.208 429 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ZHF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290055218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2395 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15669 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 37.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIMPLE REMARK 200 STARTING MODEL: PDB ENTRY 4BCX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES/IMIDAZOLE PH 6.5, 0.02 M REMARK 280 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1, 2-PROPANEDIOL, REMARK 280 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, REMARK 280 10% (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF REMARK 280 PROTEIN TO MOTHER LIQUOR), PEPTIDE WAS AT ABOUT 50 FOLD MOLAR REMARK 280 EXCESS REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 17.42050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.74200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.72850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.74200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.42050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.72850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 662 REMARK 465 ACE B 0 REMARK 465 ASN B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NH1 ARG A 746 O HOH A 2068 2.12 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 TRP A 784 -21.14 -143.31 REMARK 500 ASP B 3 158.89 -49.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 AMINO GROUP (NH2): PEPTIDE C TERMINUS IS AMIDATED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 1786 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1787 REMARK 999 REMARK 999 SEQUENCE REMARK 999 GGS IS A CLONING ARTEFACT AT THE PROTEIN N-TERMINUS DBREF 3ZHF A 665 785 UNP O75843 AP1G2_HUMAN 665 785 DBREF 3ZHF B 1 7 UNP Q67953 Q67953_HBV 85 91 SEQADV 3ZHF GLY A 662 UNP O75843 EXPRESSION TAG SEQADV 3ZHF GLY A 663 UNP O75843 EXPRESSION TAG SEQADV 3ZHF SER A 664 UNP O75843 EXPRESSION TAG SEQADV 3ZHF ACE B 0 UNP Q67953 ACETYLATION SEQADV 3ZHF NH2 B 8 UNP Q67953 AMIDATION SEQRES 1 A 124 GLY GLY SER ALA PRO ILE PRO ASP LEU LYS VAL PHE GLU SEQRES 2 A 124 ARG GLU GLY VAL GLN LEU ASN LEU SER PHE ILE ARG PRO SEQRES 3 A 124 PRO GLU ASN PRO ALA LEU LEU LEU ILE THR ILE THR ALA SEQRES 4 A 124 THR ASN PHE SER GLU GLY ASP VAL THR HIS PHE ILE CYS SEQRES 5 A 124 GLN ALA ALA VAL PRO LYS SER LEU GLN LEU GLN LEU GLN SEQRES 6 A 124 ALA PRO SER GLY ASN THR VAL PRO ALA ARG GLY GLY LEU SEQRES 7 A 124 PRO ILE THR GLN LEU PHE ARG ILE LEU ASN PRO ASN LYS SEQRES 8 A 124 ALA PRO LEU ARG LEU LYS LEU ARG LEU THR TYR ASP HIS SEQRES 9 A 124 PHE HIS GLN SER VAL GLN GLU ILE PHE GLU VAL ASN ASN SEQRES 10 A 124 LEU PRO VAL GLU SER TRP GLN SEQRES 1 B 9 ACE ASN PRO ASP TRP ASP PHE ASN NH2 HET NH2 B 8 1 HET PEG A1786 7 HET EDO A1787 4 HETNAM NH2 AMINO GROUP HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NH2 H2 N FORMUL 3 PEG C4 H10 O3 FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *84(H2 O) HELIX 1 1 PRO A 780 TRP A 784 5 5 SHEET 1 AA 5 LEU A 670 ARG A 675 0 SHEET 2 AA 5 VAL A 678 ILE A 685 -1 O VAL A 678 N ARG A 675 SHEET 3 AA 5 LEU A 693 ASN A 702 -1 O LEU A 695 N ILE A 685 SHEET 4 AA 5 ILE A 741 LEU A 748 -1 O ILE A 741 N ALA A 700 SHEET 5 AA 5 GLN A 722 LEU A 725 -1 O GLN A 722 N LEU A 748 SHEET 1 AB 3 VAL A 708 ALA A 716 0 SHEET 2 AB 3 LYS A 758 HIS A 765 -1 O LYS A 758 N ALA A 716 SHEET 3 AB 3 GLN A 768 GLU A 775 -1 O GLN A 768 N HIS A 765 LINK C ASN B 7 N NH2 B 8 1555 1555 1.32 SITE 1 AC1 1 LYS A 758 SITE 1 AC2 5 GLN A 714 ALA A 715 LEU A 725 HOH A2047 SITE 2 AC2 5 ASN B 7 CRYST1 34.841 37.457 105.484 90.00 90.00 90.00 P 21 21 21 4 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 0.028702 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009480 0.00000