[English] 日本語
Yorodumi
- PDB-1ck4: CRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ck4
TitleCRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN.
ComponentsINTEGRIN ALPHA-1
KeywordsSTRUCTURAL PROTEIN / I-DOMAIN / METAL BINDING / COLLAGEN / ADHESION
Function / homology
Function and homology information


Integrin cell surface interactions / Smooth Muscle Contraction / integrin alpha1-beta1 complex / cellular extravasation / collagen binding involved in cell-matrix adhesion / phosphatase activator activity / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway ...Integrin cell surface interactions / Smooth Muscle Contraction / integrin alpha1-beta1 complex / cellular extravasation / collagen binding involved in cell-matrix adhesion / phosphatase activator activity / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / collagen binding / neutrophil chemotaxis / acrosomal vesicle / neuron projection morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / cell chemotaxis / cell-cell adhesion / vasodilation / integrin binding / positive regulation of neuron apoptotic process / protein phosphatase binding / perikaryon / positive regulation of MAPK cascade / cell adhesion / external side of plasma membrane / signaling receptor binding / negative regulation of cell population proliferation / focal adhesion / cell surface / metal ion binding
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 ...: / Integrin alpha Ig-like domain 3 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNolte, M. / Pepinsky, R.B. / Venyaminov, S.Y. / Koteliansky, V. / Gotwals, P.J. / Karpusas, M.
CitationJournal: FEBS Lett. / Year: 1999
Title: Crystal structure of the alpha1beta1 integrin I-domain: insights into integrin I-domain function.
Authors: Nolte, M. / Pepinsky, R.B. / Venyaminov, S.Y.u. / Koteliansky, V. / Gotwals, P.J. / Karpusas, M.
History
DepositionApr 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTEGRIN ALPHA-1
B: INTEGRIN ALPHA-1


Theoretical massNumber of molelcules
Total (without water)44,2362
Polymers44,2362
Non-polymers00
Water3,873215
1
A: INTEGRIN ALPHA-1


Theoretical massNumber of molelcules
Total (without water)22,1181
Polymers22,1181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INTEGRIN ALPHA-1


Theoretical massNumber of molelcules
Total (without water)22,1181
Polymers22,1181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.770, 85.920, 132.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99929, 0.00081, 0.03763), (0.03596, 0.27445, -0.96093), (-0.01111, 0.9616, 0.27422)
Vector: -7.52793, 41.65117, -46.95238)

-
Components

#1: Protein INTEGRIN ALPHA-1


Mass: 22118.053 Da / Num. of mol.: 2 / Fragment: I-DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): DH5A / Production host: Escherichia coli (E. coli) / References: UniProt: P18614
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 4.22 Å3/Da / Density % sol: 45.03 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMTris1drop
210 mM2-mercaptoethanol1drop
311 mg/mlprotein1drop
425 %(w/v)PEG80001reservoir
50.1 Msodium cacodylate1reservoir
60.2 Msodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 19238 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 77.6 % / Mean I/σ(I) obs: 3.14

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOX

1aox


Resolution: 2.2→100 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: FOR CHAIN A, SIDE CHAINS OF RESIDUES 145, 146, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS. FOR CHAIN B, SIDE CHAINS OF RESIDUES 145, 175, 234 ARE ...Details: FOR CHAIN A, SIDE CHAINS OF RESIDUES 145, 146, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS. FOR CHAIN B, SIDE CHAINS OF RESIDUES 145, 175, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 -10 %RANDOM
Rwork0.234 ---
obs-19238 91.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 0 215 3968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
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
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

+
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