[English] 日本語
Yorodumi
- PDB-1f5w: DIMERIC STRUCTURE OF THE COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f5w
TitleDIMERIC STRUCTURE OF THE COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR D1 DOMAIN
ComponentsCOXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
KeywordsViral protein receptor / immunoglobulin V domain fold / symmetric dimer
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 / connexin binding ...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 / connexin binding / transepithelial transport / cell-cell junction organization / cardiac muscle cell development / heterophilic cell-cell adhesion / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / Cell surface interactions at the vascular wall / mitochondrion organization / filopodium / adherens junction / PDZ domain binding / neuromuscular junction / beta-catenin binding / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / cell junction / heart development / cell body / growth cone / virus receptor activity / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / neuron projection / membrane raft / signaling receptor binding / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorsvan Raaij, M.J. / Chouin, E. / van der Zandt, H. / Bergelson, J.M. / Cusack, S.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Dimeric structure of the coxsackievirus and adenovirus receptor D1 domain at 1.7 A resolution.
Authors: van Raaij, M.J. / Chouin, E. / van der Zandt, H. / Bergelson, J.M. / Cusack, S.
History
DepositionJun 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
B: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3865
Polymers28,0982
Non-polymers2883
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-35 kcal/mol
Surface area11940 Å2
MethodPISA
2
B: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
hetero molecules

A: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3865
Polymers28,0982
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y+1/2,-z+3/41
Buried area1370 Å2
ΔGint-39 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.337, 68.337, 146.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is the dimer formed by chains A and B

-
Components

#1: Protein COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR


Mass: 14048.972 Da / Num. of mol.: 2 / Fragment: D1 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HELA CELL CDNA LIBRARY / Plasmid: PAB3 / Production host: Escherichia coli (E. coli) / References: UniProt: P78310
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.3 %
Description: THE SIGMA(I) IN SCALA APPEARS TO BE OVERESTIMATED FOR OUR DATASET, GIVING LOW I/SIGMA(I) VALUES. THE Mn(I)/sd OVERALL AND FOR THE HIGH RESOLUTION SHELL ARE 10.8 AND 3.2, RESPECTIVELY TWO ...Description: THE SIGMA(I) IN SCALA APPEARS TO BE OVERESTIMATED FOR OUR DATASET, GIVING LOW I/SIGMA(I) VALUES. THE Mn(I)/sd OVERALL AND FOR THE HIGH RESOLUTION SHELL ARE 10.8 AND 3.2, RESPECTIVELY TWO MOLECULES COULD BE PLACED IN ASYMMETRIC UNIT BY MOLECULAR REPLACEMENT
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: ammonium sulphate, sodium citrate, glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate1reservoir
225 %(v/v)glycerol1reservoir
345-60 %(v/v)satammonium sulfate1reservoir
412 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC / Detector: CCD / Date: Feb 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 36389 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.079 / Net I/σ(I): 2.4
Reflection shellResolution: 1.7→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 0.4 / Rsym value: 0.375 / % possible all: 70.2
Reflection
*PLUS
Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 70.2 % / Num. unique obs: 3806 / Rmerge(I) obs: 0.302

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kac, chain B

1kac


Resolution: 1.7→20 Å / SU B: 1.45946 / SU ML: 0.04749 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.10264 / ESU R Free: 0.08305 / Stereochemistry target values: Engh & Huber
Details: PEPTIDE PLANAR RMS 0.0243 ANGSTROM; AROMATIC PLANAR RMS 0.0134 ANGSTROM
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1564 4.3 %Thin shells of resolution
Rwork0.158 ---
all0.16 ---
obs0.16 34825 90.1 %-
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 15 232 2168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.025
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_multtor_nbd0.2380.3
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_planar_d0.0340.06
X-RAY DIFFRACTIONp_mcbond_it3.2254
X-RAY DIFFRACTIONp_mcangle_it3.9625
X-RAY DIFFRACTIONp_scbond_it5.4736
X-RAY DIFFRACTIONp_scangle_it7.0868
X-RAY DIFFRACTIONp_chiral_restr0.1250.15
X-RAY DIFFRACTIONp_transverse_tor15.520
X-RAY DIFFRACTIONp_planar_tor4.45
X-RAY DIFFRACTIONp_staggered_tor13.215
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / σ(F): 0 / % reflection Rfree: 4.3 % / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it4
X-RAY DIFFRACTIONp_scbond_it6
X-RAY DIFFRACTIONp_mcangle_it5
X-RAY DIFFRACTIONp_scangle_it8
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.84 Å / Rfactor Rfree: 0.23 / Num. reflection Rfree: 222 / Num. reflection obs: 5948 / Rfactor obs: 0.15

+
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