1GL4 | pdb_00001gl4

Nidogen-1 G2/Perlecan IG3 Complex

PDB DOI: https://doi.org/10.2210/pdb1GL4/pdb

Classification: BASEMENT MEMBRANE
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2001-08-23 Released: 2001-11-28
Deposition Author(s): Kvansakul, M., Hopf, M., Ries, A., Timpl, R., Hohenester, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.247 (Depositor), 0.246 (DCC)
R-Value Work:
0.217 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis for the High-Affinity Interaction of Nidogen-1 with Immunoglobulin-Like Domain 3 of Perlecan

Kvansakul, M., Hopf, M., Ries, A., Timpl, R., Hohenester, E.

(2001) EMBO J 20: 5342

PubMed: 11574465 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/emboj/20.19.5342
Primary Citation Related Structures:
1GL4

PubMed Abstract:
Nidogen and perlecan are large multifunctional basement membrane (BM) proteins conserved in all metazoa. Their high-affinity interaction, which is likely to contribute to BM assembly and function, is mediated by the central G2 domain in nidogen and the third immunoglobulin (IG)-like domain in perlecan, IG3. We have solved the crystal structure at 2.0 A resolution of the mouse nidogen-1 G2-perlecan IG3 complex. Perlecan IG3 belongs to the I-set of the IG superfamily and binds to the wall of the nidogen-1 G2 beta-barrel using beta-strands C, D and F. Nidogen-1 residues participating in the extensive interface are highly conserved, whereas the corresponding binding site on perlecan is more variable. We hypothesize that a second, as yet unidentified, activity of nidogen overlaps with perlecan binding and accounts for the unusually high degree of surface conservation in the G2 domain.

Organizational Affiliation

Biophysics Section, Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK.

Macromolecule Content

Total Structure Weight: 42.22 kDa
Atom Count: 2,993
Modeled Residue Count: 362
Deposited Residue Count: 383
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NIDOGEN-1	A	285	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P10493 (Mus musculus) Explore P10493 Go to UniProtKB: P10493
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10493
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BASEMENT MEMBRANE-SPECIFIC HEPARAN SULFATE PROTEOGLYCAN CORE PROTEIN	B	98	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q05793 (Mus musculus) Explore Q05793 Go to UniProtKB: Q05793
IMPC: MGI:96257
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05793
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247 (Depositor), 0.246 (DCC)
R-Value Work: 0.217 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.92	α = 90
b = 72.3	β = 90
c = 103.93	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-11-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-11-28
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary