[English] 日本語
Yorodumi
- PDB-1knb: CRYSTAL STRUCTURE OF THE RECEPTOR-BINDING DOMAIN OF ADENOVIRUS TY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1knb
TitleCRYSTAL STRUCTURE OF THE RECEPTOR-BINDING DOMAIN OF ADENOVIRUS TYPE 5 FIBER PROTEIN AT 1.7 ANGSTROMS RESOLUTION
ComponentsADENOVIRUS TYPE 5 FIBER PROTEIN
KeywordsCELL RECEPTOR RECOGNITION
Function / homology
Function and homology information


viral capsid, fiber / adhesion receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsXia, D. / Henry, L.J. / Gerard, R.D. / Deisenhofer, J.
Citation
Journal: Structure / Year: 1994
Title: Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 A resolution.
Authors: Xia, D. / Henry, L.J. / Gerard, R.D. / Deisenhofer, J.
#1: Journal: J.Virol. / Year: 1994
Title: Characterization of the Knob Domain of the Adenovirus Type 5 Fiber Protein Expressed in Escherichia Coli
Authors: Henry, L.J. / Xia, D. / Wilke, M.E. / Deisenhofer, J. / Gerard, R.D.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Structure of Adenovirus Fiber: Morphology of Single Fibers
Authors: Ruigrok, R.W.H. / Barge, A. / Albiges-Rizo, C. / Dayan, S.
History
DepositionJan 6, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENOVIRUS TYPE 5 FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2571
Polymers21,2571
Non-polymers00
Water2,612145
1
A: ADENOVIRUS TYPE 5 FIBER PROTEIN

A: ADENOVIRUS TYPE 5 FIBER PROTEIN

A: ADENOVIRUS TYPE 5 FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)63,7703
Polymers63,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Unit cell
Length a, b, c (Å)86.400, 86.400, 86.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: CIS PROLINE - PRO 447

-
Components

#1: Protein ADENOVIRUS TYPE 5 FIBER PROTEIN


Mass: 21256.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Genus: Mastadenovirus / Species: Human adenovirus C / Production host: Escherichia coli (E. coli) / References: UniProt: P11818
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
22 %(v/v)PEG4001drop
330 %ammonium sulphate1drop
40.1 Mimidazol1drop
52 %(v/v)PEG4001reservoir
630 %ammonium sulphate1reservoir
70.1 Mimidazol1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→12 Å / Num. obs: 17633 / % possible obs: 73.9 % / Observed criterion σ(I): 2

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.158 / Rfactor obs: 0.158 / Highest resolution: 1.7 Å
Details: IN THE MONOMER STRUCTURE, THERE ARE TWO REGIONS WHERE B FACTORS ARE HIGH. ONE REGION IS FROM 396 - 397 WHICH IS LOCATED AT THE N-TERMINUS. THE OTHER REGION IS BETWEEN BETA STRANDS H AND I FOR RESIDUES 540 - 546.
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 0 435 2177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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

+
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