Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  HSV-1 NUCLEAR EGRESS COMPLEX
 
Authors :  J. M. Bigalke, E. E. Heldwein
Date :  20 May 15  (Deposition) - 11 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (6x)
Keywords :  Hsv-1, Nuclear Egress, Ul31, Ul34, Membrane Deformation, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Bigalke, E. E. Heldwein
Structural Basis Of Membrane Budding By The Nuclear Egress Complex Of Herpesviruses.
Embo J. V. 34 2921 2015
PubMed-ID: 26511020  |  Reference-DOI: 10.15252/EMBJ.201592359

(-) Compounds

Molecule 1 - VIRION EGRESS PROTEIN UL34
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 15-185
    Gene: UL34
    Organism Common: HHV-1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10299
    Strain: 17
    Synonym: PRIMARY ENVELOPMENT FACTOR UL34
 
Molecule 2 - VIRION EGRESS PROTEIN UL31
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 51-306
    Gene: UL31
    Organism Common: HHV-1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10299
    Strain: 17

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (6x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2NA2Ligand/IonSODIUM ION
3NI2Ligand/IonNICKEL (II) ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3NI-1Ligand/IonNICKEL (II) ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3NI-1Ligand/IonNICKEL (II) ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3NI-1Ligand/IonNICKEL (II) ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , CL A:202 , HOH A:311binding site for residue NI A 201
2AC2SOFTWARENI A:201 , HOH A:311 , HOH A:312binding site for residue CL A 202
3AC3SOFTWAREGLY A:59 , ASP A:61 , VAL A:157 , ARG A:158binding site for residue CL A 203
4AC4SOFTWARECYS B:106 , CYS B:122 , CYS B:125 , HIS B:225binding site for residue ZN B 401
5AC5SOFTWAREVAL B:102 , ALA B:103 , ASN B:105 , TYR B:228 , ILE B:231 , ASP B:232binding site for residue NA B 402
6AC6SOFTWAREARG C:32 , HIS C:55 , HIS C:57 , CL C:202 , HOH C:302 , HOH C:313binding site for residue NI C 201
7AC7SOFTWARENI C:201 , HOH C:313binding site for residue CL C 202
8AC8SOFTWARECYS D:106 , CYS D:122 , CYS D:125 , HIS D:225binding site for residue ZN D 401
9AC9SOFTWAREPHE D:219 , GLY D:221 , THR D:251 , PHE D:252binding site for residue NA D 402

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:278 -D:278

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:159 -Pro A:160
2Leu B:94 -Pro B:95
3Met C:159 -Pro C:160
4Leu D:94 -Pro D:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZXS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZXS)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZXS)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eeee...............eeeee....eeeehhhhhhhhhhhhh......eeeeee....eeeeee................eeee...eeeeeehhhhhhhhhhh.........eeeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zxs A  14 PAFEGLVQRIRLIVPSTLRGGDGEGPYSPSSLPSRCAFQFHGHDGSDESFPIEYVLRLMNDWAEVPCNPYLRIQNTGVSVLFQGFFHRPHNPGGAITPERTNVILGSTETTGLSLGDLDTIKGRLGLDARPMMASMWISCFVRMPRVQLAFRFMGPEDA 174
                                    23        33   ||   44        54        64        74        84        94       104||     115       125       135       145       155       165         
                                                  37|                                                               105|                                                                   
                                                   39                                                                107                                                                   


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.ee...eee....ee.hhh...eeeeee..eeeeee...hhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhh......eeeeee......eeeeee.....eeehhhhhhhhhhhh..eeeeeeee..eeeeeeee.....hhhhhhhhhhhh....hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zxs B  55 LHERQRYRGLFAALAQTPSEEIAIVRSLSVPLVKTTPVSLPFCLDQTVADNCLTLSGMGYYLGIGGCCPACNAGDGAATSREALILAFVQQINTIFEHRAFLASLVVLADRHNAPLQDLLAGILGQPELFFVHTILRGGGACDPRLLFYPDPTYGGHMLYVIFPGTSAHLHYRLIDRMLTACPGYRFVAHVWQSTFVLVVRRNAPTVSAADIYCKMRDISFDGGLMLEYQRLYATFDEFPPP 306
                                    64        74        84        94       104       114       124     ||136       146       156       166       176       186       196       206       216       226       236       246       256   ||  274       284       294       304  
                                                                                                     130|                                                                                                                            260|                                     
                                                                                                      133                                                                                                                             269                                     


Chain C from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eeee................eeeee....eeeehhhhhhhhhhhhh......eeeeee....eeeeee................eeee...eeeeeehhhhhhhhhhh.........eeeeeeeee..eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zxs C  14 PAFEGLVQRIRLIVPSTLRGGDGEAGPYSPSSLPSRCAFQFHGHDGSDESFPIEYVLRLMNDWAEVPCNPYLRIQNTGVSVLFQGFFHRPHNAGGAITPERTNVILGSTETTGLSLGDLDTIKGRLGLDARPMMASMWISCFVRMPRVQLAFRFMGPEDAG 175
                                    23        33        43        53        63        73        83        93       103  ||   114       124       134       144       154       164       174 
                                                                                                                      106|                                                                   
                                                                                                                       108                                                                   


Chain D from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.ee...eee....ee.hhh...eeeeee..eeeeee...hhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh......eeeeee......eeeeee.....eeehhhhhhhhhhhh..eeeeeeee..eeeeeeee.......hhhhhhhhhhh....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zxs D  55 LHERQRYRGLFAALAQTPSEEIAIVRSLSVPLVKTTPVSLPFCLDQTVADNCLTLSGMGYYLGIGGCCPACNAGATSREALILAFVQQINTIFEHRAFLASLVVLADRHNAPLQDLLAGILGQPELFFVHTILRGGGACDPRLLFYPDPTYGGHMLYVIFPGTSAHLHYRLIDRMLTACPGYRFVAHVWQSTFVLVVRRNAEKPTVSAADIYCKMRDISFDGGLMLEYQRLYATFDEFPPP 306
                                    64        74        84        94       104       114       124   ||  139       149       159       169       179       189       199       209       219       229       239       249       259  ||   275       285       295       305 
                                                                                                   128|                                                                                                                             262|                                     
                                                                                                    134                                                                                                                              269
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4ZXS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZXS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZXS)

(-) Gene Ontology  (7, 13)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu B:94 - Pro B:95   [ RasMol ]  
    Leu D:94 - Pro D:95   [ RasMol ]  
    Met A:159 - Pro A:160   [ RasMol ]  
    Met C:159 - Pro C:160   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4zxs
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NEC1_HHV11 | P10215
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  NEC2_HHV11 | P10218
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NEC1_HHV11 | P10215
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NEC2_HHV11 | P10218
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 4ZXS)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZXS)