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
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)

(-) Description

Title :  HUMAN ACTIN-RELATED PROTEIN ARP8 IN ITS ATP-BOUND STATE
 
Authors :  C. B. Gerhold, K. Lakomek, F. U. Seifert, K. -P. Hopfner
Date :  20 Jun 12  (Deposition) - 26 Sep 12  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Actin-Related Protein, Chromatin Remodeling, Nucleosomes, Nucleus, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. B. Gerhold, D. D. Winkler, K. Lakomek, F. U. Seifert, S. Fenn, B. Kessler, G. Witte, K. Luger, K. P. Hopfner
Structure Of Actin-Related Protein 8 And Its Contribution T Nucleosome Binding.
Nucleic Acids Res. V. 40 11036 2012
PubMed-ID: 22977180  |  Reference-DOI: 10.1093/NAR/GKS842

(-) Compounds

Molecule 1 - ACTIN-RELATED PROTEIN 8
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28
    Expression System Strain: ROSETTA 2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HARP8, INO80 COMPLEX SUBUNIT N

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3GOL8Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL8Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 18)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL16Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:288 , ATP A:702 , HOH A:844 , HOH A:901 , HOH A:905 , HOH A:907BINDING SITE FOR RESIDUE MG A 701
02AC2SOFTWAREGLY A:54 , SER A:55 , THR A:56 , THR A:57 , ARG A:59 , GLY A:285 , ASP A:286 , GLN A:287 , LYS A:288 , GLY A:311 , GLN A:344 , LYS A:347 , GLU A:348 , GLY A:539 , GLY A:540 , GLY A:541 , MET A:543 , PHE A:544 , MG A:701 , HOH A:809 , HOH A:813 , HOH A:814 , HOH A:815 , HOH A:844 , HOH A:845 , HOH A:901 , HOH A:930BINDING SITE FOR RESIDUE ATP A 702
03AC3SOFTWAREGLN A:105 , PRO A:395 , ALA A:396 , PHE A:398 , GLY A:399 , ILE A:400 , MET A:405 , ALA A:508BINDING SITE FOR RESIDUE GOL A 703
04AC4SOFTWAREGLY A:153 , ASN A:154 , LYS A:155 , TYR A:173 , HOH A:823 , HOH A:940BINDING SITE FOR RESIDUE GOL A 704
05AC5SOFTWAREGLN A:107 , LEU A:110 , LYS A:111 , ASP A:114 , ASP A:149 , HIS A:150 , HOH A:871BINDING SITE FOR RESIDUE GOL A 705
06AC6SOFTWARETYR A:329 , GLU A:331 , GLN A:333 , ASP A:339 , HOH A:939BINDING SITE FOR RESIDUE GOL A 706
07AC7SOFTWAREPHE A:350 , HIS A:363 , LYS A:385BINDING SITE FOR RESIDUE GOL A 707
08AC8SOFTWARETRP A:156 , THR A:157 , ASN A:158 , THR A:159 , SER A:160 , ASN A:175 , ASP A:178 , HOH A:919BINDING SITE FOR RESIDUE GOL A 708
09AC9SOFTWAREPRO A:176 , THR A:335 , ASN A:336 , LYS A:337 , MET A:338 , HOH A:842 , HOH A:929BINDING SITE FOR RESIDUE GOL A 709
10BC1SOFTWAREGLN A:44 , SER A:45 , ALA A:593 , CYS A:594BINDING SITE FOR RESIDUE GOL A 710
11BC2SOFTWAREMET A:579 , ASP A:580 , LYS A:587BINDING SITE FOR RESIDUE CL A 711

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FO0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FO0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FO0)

(-) Exons   (0, 0)

(no "Exon" information available for 4FO0)

(-) 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:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeee..eeeeee....eeeeee..eeeee......eeeeee.........hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.eeeeeee..............eeeehhhhhh......eeeee................hhhhhhhhhhhhhhhhhhh....hhhhhh.eeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhhhhhh...eeeeeee....eeeeeee........eeee..hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.........eeeeeee......eeeeeeee.hhhhhhhhhhh............eeee..hhhhh...hhhhhhhhhhh...hhhhhhhhheeeee........hhhhhhhhhhhhh.hhhhhhh..eeeee........hhhhhhhhhhhh.hhhhhh...hhhhhhh.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fo0 A  32 GPLVPESLQEQIQSNFIIVIHPGSTTLRIGRATDTLPASIPHVIARRHKQQGQPLYKDSWLLREGLNKPESNEQRQNGLKMVDQAIWSKKMSNGTRRIPVSPEQARSYNKQMRPAILDHCSGNKWTNTSHHPEYLVGEEALYVNPLDCYNIHWPIRRGQLNIHPGPGGSLTAVLADIEVIWSHAIQKYLEIPLKDLKYYRCILLIPDIYNKQHVKELVNMILMKMGFSGIVVHQESVCATYGSGLSSTCIVDVGDQKTSVCCVEDGVSHRNTRLCLAYGGSDVSRCFYWLMQRAGFPYRECQLTNKMDCLLLQHLKETFCHLDQDISGLQDHEFQIRHPDSPALLYQFRLGDEKLQAPMALFYPATFGIVGQKMTTLQHSLFEGKALGLDKAILHSIDCCSSDDTKKKMYSSILVVGGGLMFHKAQEFLQHRILNKMPPSFRRIIENVDVITRPKDMDPRLIAWKGGAVLACLDTTQELWIYQREWQRFGVRMLRERAAFVW 624
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       502       512       522       532       542       552       562       572       582       592       602       612       622  
                                                                                                                                                                                                                                                                                                                                                                                                                    410|                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                     502
   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 4FO0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FO0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FO0)

(-) Gene Ontology  (15, 15)

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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fo0)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  4fo0
    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
  ARP8_HUMAN | Q9H981
    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
  ARP8_HUMAN | Q9H981
    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 4FO0)

(-) Related Entries Specified in the PDB File

3qb0 CRYSTAL STRUCTURE OF ACTIN-RELATED PROTEIN ARP4 FROM S. CEREVISIAE COMPLEXED WITH ATP