[English] 日本語
Yorodumi
- PDB-1adu: EARLY E2A DNA-BINDING PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1adu
TitleEARLY E2A DNA-BINDING PROTEIN
ComponentsADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / SSDNA BINDING PROTEIN
Function / homology
Function and homology information


viral DNA strand displacement replication / viral DNA genome replication / DNA duplex unwinding / DNA unwinding involved in DNA replication / positive regulation of DNA replication / viral capsid / single-stranded DNA binding / DNA-templated transcription / host cell nucleus / DNA binding ...viral DNA strand displacement replication / viral DNA genome replication / DNA duplex unwinding / DNA unwinding involved in DNA replication / positive regulation of DNA replication / viral capsid / single-stranded DNA binding / DNA-templated transcription / host cell nucleus / DNA binding / zinc ion binding / identical protein binding
Similarity search - Function
Adenovirus Single-stranded Dna-binding Protein, domain 1 / Adenovirus DNA-binding, N-terminal domain / Adenovirus Single-stranded DNA-binding Protein; domain 2 / Adenovirus DNA-binding, C-terminal domain superfamily/Adenovirus DNA-binding, zinc binding domain / Adenovirus DNA-binding, all-alpha domain / Adenovirus DNA-binding, zinc-binding domain / Adenovirus DNA-binding, N-terminal domain superfamily / Adenovirus DNA-binding, C-terminal domain superfamily / Adenovirus DNA-binding, zinc binding domain superfamily / DNA-binding protein, Adenovirus ...Adenovirus Single-stranded Dna-binding Protein, domain 1 / Adenovirus DNA-binding, N-terminal domain / Adenovirus Single-stranded DNA-binding Protein; domain 2 / Adenovirus DNA-binding, C-terminal domain superfamily/Adenovirus DNA-binding, zinc binding domain / Adenovirus DNA-binding, all-alpha domain / Adenovirus DNA-binding, zinc-binding domain / Adenovirus DNA-binding, N-terminal domain superfamily / Adenovirus DNA-binding, C-terminal domain superfamily / Adenovirus DNA-binding, zinc binding domain superfamily / DNA-binding protein, Adenovirus / Viral DNA-binding protein, all alpha domain / Viral DNA-binding protein, zinc binding domain / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsTucker, P.A. / Kanellopoulos, P.N. / Tsernoglou, D. / Van Der Vliet, P.C.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Alternative arrangements of the protein chain are possible for the adenovirus single-stranded DNA binding protein.
Authors: Kanellopoulos, P.N. / Tsernoglou, D. / van der Vliet, P.C. / Tucker, P.A.
#1: Journal: Embo J. / Year: 1994
Title: Crystal Structure of the Adenovirus DNA Binding Protein Reveals a Hook-on Model for Cooperative DNA Binding
Authors: Tucker, P.A. / Tsernoglou, D. / Tucker, A.D. / Coenjaerts, F.E. / Leenders, H. / Van Der Vliet, P.C.
History
DepositionMay 11, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_conn / struct_keywords / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
B: ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0616
Polymers79,7992
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-15 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 91.200, 149.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE MOLECULES FORM CHAINS ALONG THE CRYSTALLOGRAPHIC Z AXIS. PAIRS OF MOLECULES IN THE CHAIN ARE RELATED BY A CRYSTALLOGRAPHIC SCREW AXIS.

-
Components

#1: Protein ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN / ADDBP


Mass: 39899.746 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 174 - 529 / Source method: isolated from a natural source / Details: SECOND CRYSTAL FORM, DATA COLLECTED AT 293 K / Source: (natural) Human adenovirus 5 / Genus: Mastadenovirus / Cell: INFECTED HELA CELLS / Species: Human adenovirus C / References: UniProt: P03265
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 %protein1drop
213 %satammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 27, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 17172 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.168
Reflection
*PLUS
Num. measured all: 73641
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.2 Å / Rmerge(I) obs: 0.496

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 3→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.296 -10 %
Rwork0.201 --
obs0.201 14986 86.8 %
Displacement parametersBiso mean: 35.45 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 4 0 4534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.318
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_deg

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more