[English] 日本語
Yorodumi
- PDB-3f7r: First pair of Fibronectin type III domains and part of the connec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f7r
TitleFirst pair of Fibronectin type III domains and part of the connecting segment of the integrin beta4
ComponentsIntegrin beta-4
KeywordsCELL ADHESION / INTEGRIN / HEMIDESMOSOME / CARCINOMA / EPIDERMOLYSIS BULLOSA / Alternative splicing / Disease mutation / Glycoprotein / Membrane / Phosphoprotein / Polymorphism / Receptor / Transmembrane
Function / homology
Function and homology information


trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation ...trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation / integrin complex / Assembly of collagen fibrils and other multimeric structures / cell adhesion mediated by integrin / Syndecan interactions / cell leading edge / basement membrane / basal plasma membrane / cell-matrix adhesion / G protein-coupled receptor binding / integrin-mediated signaling pathway / cell motility / autophagy / cell-cell adhesion / response to wounding / integrin binding / cell junction / nuclear membrane / receptor complex / cell adhesion / focal adhesion / nucleolus / cell surface / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-4 subunit / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Integrin beta-4 subunit / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Integrin beta-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.036 Å
Authorsde Pereda, J.M.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis of the interaction between integrin alpha6beta4 and plectin at the hemidesmosomes
Authors: de Pereda, J.M. / Lillo, M.P. / Sonnenberg, A.
History
DepositionNov 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9065
Polymers27,5961
Non-polymers3104
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.500, 42.150, 56.910
Angle α, β, γ (deg.)90.00, 109.92, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Integrin beta-4 / GP150


Mass: 27595.871 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III, residues 1126-1370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB4 / Plasmid: Derivative of pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16144
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ITB4_HUMAN, RESPECTIVELY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Cacodylate, 18.75% PEG 600, 6.25% Glycerol, 0.7M NaCl, pH 6.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 26, 2005
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.036→35.674 Å / Num. all: 19573 / Num. obs: 19563 / % possible obs: 98.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31.6 Å2 / Net I/σ(I): 16.6
Reflection shellResolution: 2.036→2.11 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.6 / % possible all: 85.9

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QG3

1qg3


Resolution: 2.036→35.674 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 998 5.1 %RANDOM
Rwork0.176 18565 --
all0.178 19567 --
obs0.178 19563 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.661 Å2 / ksol: 0.432 e/Å3
Displacement parametersBiso max: 107.53 Å2 / Biso mean: 26.53 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1--4.5456 Å20 Å2-0.2221 Å2
2--6.1672 Å20 Å2
3----2.1554 Å2
Refinement stepCycle: LAST / Resolution: 2.036→35.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 5 156 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123440
X-RAY DIFFRACTIONf_angle_d1.136228
X-RAY DIFFRACTIONf_chiral_restr0.094253
X-RAY DIFFRACTIONf_plane_restr0.007540
X-RAY DIFFRACTIONf_dihedral_angle_d17.599883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0361-2.14350.28141400.24872506X-RAY DIFFRACTION94
2.1435-2.27770.24071270.18652635X-RAY DIFFRACTION98
2.2777-2.45360.21151420.17322644X-RAY DIFFRACTION98
2.4536-2.70040.21861250.16362660X-RAY DIFFRACTION99
2.7004-3.0910.1941560.15162659X-RAY DIFFRACTION99
3.091-3.89350.17251540.14622692X-RAY DIFFRACTION100
3.8935-35.67980.21651540.17182769X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0685-0.2881-0.3846-0.04190.44770.809-0.0099-0.03820.08250.0503-0.04-0.031-0.0339-0.2724-0.00040.1769-0.0071-0.00760.17080.01290.1251-12.3166-2.951444.2208
20.87340.00760.40.551-0.46160.4492-0.0286-0.0523-0.26140.033-0.0089-0.12780.03530.201500.1181-0.01810.00790.17320.00140.1815-21.6132-16.12697.2893
30.1679-0.00980.07390.1444-0.02180.06680.0901-0.0584-0.0556-0.11350.05050.0935-0.2721-0.0608-0.00010.1812-0.00710.0010.17390.05420.274-28.8039-12.03555.2536
40.14210.1675-0.20940.3343-0.10020.0193-0.1704-0.0733-0.3032-0.23880.0520.1134-0.0874-0.0579-0.00050.1776-0.0143-0.02280.0951-0.01050.1764-24.0623-16.0864-1.62
5-0.05020.2955-0.33240.65370.1101-0.0533-0.0649-0.1103-0.1216-0.03-0.0153-0.0428-0.0131-0.023100.1890.00870.0090.1372-0.01360.2148-27.9371-19.42352.4084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 1126-1216
2X-RAY DIFFRACTION2chain A and resseq 1217-1266
3X-RAY DIFFRACTION3chain A and resseq 1267-1282
4X-RAY DIFFRACTION4chain A and resseq 1283-1301
5X-RAY DIFFRACTION5chain A and resseq 1302-1339

+
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://pdbjlvh1.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