[English] 日本語
Yorodumi
- PDB-1npe: Crystal structure of Nidogen/Laminin Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1npe
TitleCrystal structure of Nidogen/Laminin Complex
Components
  • Laminin gamma-1 chain
  • nidogen
KeywordsSTRUCTURAL PROTEIN / Glycoprotein / Basement membrane / beta-propeller / EGF-like
Function / homology
Function and homology information


Laminin interactions / laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / hemidesmosome assembly / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway ...Laminin interactions / laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / hemidesmosome assembly / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / glycosphingolipid binding / Degradation of the extracellular matrix / Wnt receptor activity / tissue development / Wnt-protein binding / hair cell differentiation / protein complex involved in cell-matrix adhesion / extracellular matrix binding / positive regulation of cell-substrate adhesion / proteoglycan binding / extracellular matrix structural constituent / hair follicle morphogenesis / positive regulation of muscle cell differentiation / canonical Wnt signaling pathway / basement membrane / positive regulation of cell adhesion / extracellular matrix disassembly / synaptic cleft / laminin binding / collagen binding / extracellular matrix / extracellular matrix organization / cell-matrix adhesion / substrate adhesion-dependent cell spreading / cell periphery / animal organ morphogenesis / neuromuscular junction / neuron projection development / cell migration / gene expression / chromatin organization / collagen-containing extracellular matrix / protein-containing complex assembly / cell adhesion / calcium ion binding / extracellular region
Similarity search - Function
NIDO domain / G2 nidogen/fibulin G2F / Nidogen-like / G2F domain / Nidogen G2 beta-barrel domain profile. / NIDO domain profile. / Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins. / G2 nidogen domain and fibulin / Laminin IV / Laminin B (Domain IV) ...NIDO domain / G2 nidogen/fibulin G2F / Nidogen-like / G2F domain / Nidogen G2 beta-barrel domain profile. / NIDO domain profile. / Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins. / G2 nidogen domain and fibulin / 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) / EGF domain / EGF domain / Complement Clr-like EGF domain / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Complement Clr-like EGF-like / Laminin-type EGF domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / TolB, C-terminal domain / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / 6 Propeller / Neuraminidase / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Green fluorescent protein / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
: / Laminin subunit gamma-1 / Nidogen-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTakagi, J. / Yang, Y.T. / Liu, J.-H. / Wang, J.-H. / Springer, T.A.
CitationJournal: Nature / Year: 2003
Title: Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface
Authors: Takagi, J. / Yang, Y.T. / Liu, J.-H. / Wang, J.-H. / Springer, T.A.
History
DepositionJan 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _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: nidogen
B: Laminin gamma-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0398
Polymers47,3652
Non-polymers6746
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-34 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.180, 75.830, 104.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein nidogen / / Entactin


Mass: 29998.078 Da / Num. of mol.: 1
Fragment: G3 YWTD domain, sequence database residue 941-1203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: NID or NID1 or ENT / Plasmid: pCEP-Pu / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: P02468, UniProt: P10493*PLUS
#2: Protein Laminin gamma-1 chain / Laminin B2 chain


Mass: 17366.607 Da / Num. of mol.: 1
Fragment: modules III 3-5, sequence database residue 769-932
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LAMC1 / Plasmid: pCEP4 / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: P10493, UniProt: P02468*PLUS
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M NaAc, 0.05 M CdSO4, 0.1 M, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mg/mlprotein1drop
21 Msodium acetate1reservoir
30.05 M1reservoirCdSO4
40.1 MHEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 25891 / Num. obs: 25885 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2375 / % possible all: 92.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 25940 / % possible obs: 99 % / Num. measured all: 466114
Reflection shell
*PLUS
% possible obs: 92.5 % / Mean I/σ(I) obs: 2.7

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1IJQ and 1KLO
Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2545 -RANDOM
Rwork0.223 ---
all-25885 --
obs-25858 99 %-
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.581 Å20 Å20 Å2
2---2.96 Å20 Å2
3----2.621 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 6 127 3409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.46064
X-RAY DIFFRACTIONc_bond_d0.006444
X-RAY DIFFRACTIONc_dihedral_angle_d25.43769
X-RAY DIFFRACTIONc_improper_angle_d1.24641
Refinement
*PLUS
Rfactor Rfree: 0.257 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.43769
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24641

+
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