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- PDB-1gl4: Nidogen-1 G2/Perlecan IG3 Complex -

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Basic information

Entry
Database: PDB / ID: 1gl4
TitleNidogen-1 G2/Perlecan IG3 Complex
Components
  • BASEMENT MEMBRANE-SPECIFIC HEPARAN SULFATE PROTEOGLYCAN CORE PROTEIN
  • NIDOGEN-1
KeywordsBASEMENT MEMBRANE / IMMUNOGLOBULIN-LIKE DOMAIN / EXTRACELLULAR MATRIX / PROTEOGLYCAN / HEPARAN SULFATE
Function / homology
Function and homology information


Laminin interactions / regulation of basement membrane organization / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / Degradation of the extracellular matrix / embryonic skeletal system morphogenesis / cartilage development involved in endochondral bone morphogenesis / endochondral ossification / protein complex involved in cell-matrix adhesion ...Laminin interactions / regulation of basement membrane organization / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / Degradation of the extracellular matrix / embryonic skeletal system morphogenesis / cartilage development involved in endochondral bone morphogenesis / endochondral ossification / protein complex involved in cell-matrix adhesion / extracellular matrix binding / proteoglycan binding / cardiac muscle tissue development / positive regulation of cell-substrate adhesion / positive regulation of muscle cell differentiation / basement membrane / chondrocyte differentiation / collagen binding / extracellular matrix organization / extracellular matrix / positive regulation of cell adhesion / receptor-mediated endocytosis / cell-matrix adhesion / cell periphery / brain development / Golgi lumen / intracellular protein localization / : / protease binding / angiogenesis / 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 ...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 / EGF domain / EGF domain / : / Laminin/attractin EGF domain / : / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Thyroglobulin type-1 repeat signature. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Domain found in sea urchin sperm protein, enterokinase, agrin / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Complement Clr-like EGF domain / Laminin-type EGF domain / Complement Clr-like EGF-like / SEA domain profile. / SEA domain / Laminin G domain profile. / Laminin G domain / Laminin G 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 / Low-density lipoprotein receptor domain class A / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Green Fluorescent Protein / Green fluorescent protein / EGF-like domain / Immunoglobulin domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / Green fluorescent protein / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nidogen-1 / Basement membrane-specific heparan sulfate proteoglycan core protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKvansakul, M. / Hopf, M. / Ries, A. / Timpl, R. / Hohenester, E.
Citation
Journal: Embo J. / Year: 2001
Title: Structural Basis for the High-Affinity Interaction of Nidogen-1 with Immunoglobulin-Like Domain 3 of Perlecan
Authors: Kvansakul, M. / Hopf, M. / Ries, A. / Timpl, R. / Hohenester, E.
#1: Journal: Nat.Struct.Biol . / Year: 2001
Title: Crystal Structure and Mutational Analysis of a Perlecan-Binding Fragment of Nidogen-1
Authors: Hopf, M. / Gohring, W. / Ries, A. / Timpl, R. / Hohenester, E.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: Mapping of Binding Sites for Nidogens, Fibulin-2, Fibronectin and Heparin to Different Ig Modules of Perlecan
Authors: Hopf, M. / Gohring, W. / Mann, K. / Timpl, R.
History
DepositionAug 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: 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 / 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 / _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_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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NIDOGEN-1
B: BASEMENT MEMBRANE-SPECIFIC HEPARAN SULFATE PROTEOGLYCAN CORE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2174
Polymers41,9132
Non-polymers3042
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.920, 72.300, 103.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NIDOGEN-1 / ENTACTIN


Mass: 31350.930 Da / Num. of mol.: 1 / Fragment: G2 RESIDUES 385-665
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: P10493
#2: Protein BASEMENT MEMBRANE-SPECIFIC HEPARAN SULFATE PROTEOGLYCAN CORE PROTEIN / PERLECAN / HSPG / PLC


Mass: 10562.085 Da / Num. of mol.: 1 / Fragment: IG3 RESIDUES 1765-1858
Source method: isolated from a genetically manipulated source
Details: VECTOR-DERIVED N-TERMINAL APLA / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: VECTOR-DERIVED N-TERMINAL APLA / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: Q05793
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 7.5 / Details: 10% PEG 6000, 5% MPD, 0.1 M HEPES PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
20.04 Mammonium acetate1droppH6.8
310 %PEG60001reservoir
45 %MPD1reservoir
50.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: QUANTUM4 / Detector: CCD / Date: Nov 6, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 29096 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H4U

1h4u


Resolution: 2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2898 10 %RANDOM
Rwork0.217 ---
obs0.217 29096 99.8 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 16 174 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.288
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_it1.3581.5
X-RAY DIFFRACTIONc_mcangle_it2.0722
X-RAY DIFFRACTIONc_scbond_it2.1942
X-RAY DIFFRACTIONc_scangle_it3.1932.5
LS refinement shellResolution: 2→2.01 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.234 59 10 %
Rwork0.228 511 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor obs: 0.21 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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