[English] 日本語
Yorodumi
- PDB-1kac: KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kac
TitleKNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 OF ITS CELLULAR RECEPTOR CAR
Components
  • PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)
  • PROTEIN (FIBER KNOB PROTEIN)
KeywordsViral protein/receptor / ADHESION PROTEIN RECEPTOR COMPLEX / VIRAL PROTEIN-RECEPTOR COMPLEX
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / cardiac muscle fiber development / cell-cell junction organization / negative regulation of cardiac muscle cell proliferation / connexin binding / adhesion receptor-mediated virion attachment to host cell / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / intercalated disc / bicellular tight junction / actin cytoskeleton reorganization / acrosomal vesicle / mitochondrion organization / filopodium / cell adhesion molecule binding / PDZ domain binding / neutrophil chemotaxis / adherens junction / neuromuscular junction / beta-catenin binding / virus receptor activity / cell body / viral capsid / cell junction / cell-cell junction / growth cone / integrin binding / defense response to virus / regulation of immune response / heart development / leukocyte migration / basolateral plasma membrane / viral entry into host cell / cell adhesion / neuron projection / membrane raft / host cell nucleus / signaling receptor binding / integral component of plasma membrane / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Adenovirus fibre protein / Immunoglobulin V-set domain / Immunoglobulin-like domain / Adenovirus pIV-like, attachment domain / Adenoviral fibre protein, repeat/shaft region / Immunoglobulin subtype 2 / Adenoviral fibre protein, knob / Immunoglobulin subtype / Attachment protein shaft domain superfamily / Immunoglobulin ...Adenovirus fibre protein / Immunoglobulin V-set domain / Immunoglobulin-like domain / Adenovirus pIV-like, attachment domain / Adenoviral fibre protein, repeat/shaft region / Immunoglobulin subtype 2 / Adenoviral fibre protein, knob / Immunoglobulin subtype / Attachment protein shaft domain superfamily / Immunoglobulin / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Adenoviral fibre protein (knob domain) / Immunoglobulin V-set domain / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Fiber protein / Coxsackievirus and adenovirus receptor
Biological speciesHuman adenovirus 12
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsBewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
CitationJournal: Science / Year: 1999
Title: Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR.
Authors: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)33,5852
Polymers33,5852
Non-polymers00
Water1,26170
1
A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)

A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)

A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)100,7556
Polymers100,7556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Unit cell
γ
α
β
Length a, b, c (Å)167.850, 167.850, 167.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

-
Components

#1: Protein PROTEIN (FIBER KNOB PROTEIN)


Mass: 19944.477 Da / Num. of mol.: 1 / Fragment: KNOB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 12 / Genus: Mastadenovirus / Species: Human adenovirus A / Variant: SEROTYPE 12 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / Variant (production host): T7 / References: UniProt: P36711
#2: Protein PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)


Mass: 13640.500 Da / Num. of mol.: 1 / Fragment: DOMAIN 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P78310
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.6 Å3/Da / Density % sol: 78 %
Crystal growpH: 6.2 / Details: 900MM AMMONIUM SULPHATE ON 100MM MES, PH 6.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.9 Mammonium sulfate1reservoir
2100 mMMES1reservoirpH6.2

-
Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 24636 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.7
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.35 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
AMoREphasing
CNS5refinement
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.6→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 739 2.9 %RANDOM
Rwork0.22 ---
Obs0.22 24601 96.8 %-
Solvent computationBsol: 61 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 0 70 2430
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM
Software
*PLUS
Name: CNS / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2.9 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.9 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.7

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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