[English] 日本語
Yorodumi
- PDB-2jd4: Mouse laminin alpha1 chain, domains LG4-5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jd4
TitleMouse laminin alpha1 chain, domains LG4-5
ComponentsLAMININ SUBUNIT ALPHA-1
KeywordsMETAL BINDING PROTEIN / LAMININ-111 / BASEMENT MEMBRANE PROTEIN
Function / homology
Function and homology information


laminin-3 complex / laminin complex / laminin-1 complex / regulation of basement membrane organization / retinal blood vessel morphogenesis / morphogenesis of an epithelial sheet / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion ...laminin-3 complex / laminin complex / laminin-1 complex / regulation of basement membrane organization / retinal blood vessel morphogenesis / morphogenesis of an epithelial sheet / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion / branching involved in salivary gland morphogenesis / establishment of epithelial cell apical/basal polarity / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / epithelial tube branching involved in lung morphogenesis / basement membrane / regulation of embryonic development / extracellular matrix / positive regulation of cell adhesion / regulation of cell migration / neuron projection development / cell-cell junction / : / retina development in camera-type eye / cell surface receptor signaling pathway / protein phosphorylation / cell adhesion / signaling receptor binding / extracellular space / extracellular region / membrane
Similarity search - Function
Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : ...Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / : / Laminin/attractin EGF domain / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Laminin subunit alpha-1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarrison, D. / Hussain, S.A. / Combs, A.C. / Ervasti, J.M. / Yurchenco, P.D. / Hohenester, E.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure and Cell Surface Anchorage Sites of Laminin {Alpha}1Lg4-5.
Authors: Harrison, D. / Hussain, S.A. / Combs, A.C. / Ervasti, J.M. / Yurchenco, P.D. / Hohenester, E.
#1: Journal: Embo J. / Year: 2000
Title: Structure of the C-Terminal Laminin G-Like Domain Pair of the Laminin Alpha2 Chain Harbouring Binding Sites for Alpha-Dystroglycan and Heparin
Authors: Tisi, D. / Talts, J.F. / Timpl, R. / Hohenester, E.
#2: Journal: Annu.Rev.Cell Dev.Biol. / Year: 2004
Title: Laminin Functions in Tissue Morphogenesis
Authors: Miner, J.H. / Yurchenco, P.D.
History
DepositionJan 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LAMININ SUBUNIT ALPHA-1
B: LAMININ SUBUNIT ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0079
Polymers83,8032
Non-polymers2047
Water5,891327
1
A: LAMININ SUBUNIT ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9864
Polymers41,9021
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LAMININ SUBUNIT ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0215
Polymers41,9021
Non-polymers1204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.530, 55.812, 100.986
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein LAMININ SUBUNIT ALPHA-1 / LAMININ ALPHA1 CHAIN / LAMININ A CHAIN


Mass: 41901.543 Da / Num. of mol.: 2 / Fragment: DOMAINS LG4-5, RESIDUES 2706-3084 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P19137
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 2738 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 2835 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, ASN 2738 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 2835 TO LYS ENGINEERED RESIDUE IN CHAIN A, ASN 2924 TO GLN ENGINEERED RESIDUE IN CHAIN A, CYS 3038 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 2738 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN 2835 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASN 2924 TO GLN ENGINEERED RESIDUE IN CHAIN B, CYS 3038 TO SER
Has protein modificationY
Sequence detailsVECTOR-DERIVED APLA SEQUENCE AT N-TERMINUS, GLYCOSYLATION SITES AND LONE CYSTEINE MUTATED ...VECTOR-DERIVED APLA SEQUENCE AT N-TERMINUS, GLYCOSYLATION SITES AND LONE CYSTEINE MUTATED (N2714Q,N2811K,N2900Q, C3014S)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.02 %
Crystal growpH: 8.5 / Details: pH 8.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 156499 / % possible obs: 97.3 % / Observed criterion σ(I): 4 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DYK

1dyk


Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 3015 4.9 %RANDOM
Rwork0.2295 ---
obs0.2295 59670 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1583 Å2 / ksol: 0.334241 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.788 Å20 Å21.561 Å2
2--2.828 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 7 327 6115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005521
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_deg1.35369
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_it1.962
X-RAY DIFFRACTIONc_mcangle_it3.463
X-RAY DIFFRACTIONc_scbond_it2.73
X-RAY DIFFRACTIONc_scangle_it4.764
LS refinement shellResolution: 1.9→1.91 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3434 51 5 %
Rwork0.3135 1001 -

+
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