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- PDB-1npe: Crystal structure of Nidogen/Laminin Complex -

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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 / glomerular basement membrane development / hemidesmosome assembly / laminin-1 binding / glycosphingolipid binding ...Laminin interactions / laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / glomerular basement membrane development / hemidesmosome assembly / laminin-1 binding / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / Degradation of the extracellular matrix / Wnt receptor activity / tissue development / hair cell differentiation / Wnt-protein binding / 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 / basement membrane / extracellular matrix disassembly / canonical Wnt signaling pathway / synaptic cleft / collagen binding / positive regulation of cell adhesion / cell-matrix adhesion / extracellular matrix organization / extracellular matrix / axon guidance / cell periphery / animal organ morphogenesis / neuromuscular junction / neuron projection development / cell migration / chromatin organization / gene expression / protein-containing complex assembly / collagen-containing extracellular matrix / cell adhesion / calcium ion binding / extracellular region / plasma membrane
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 / EGF domain / EGF domain / Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / : / 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 / 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 / TolB, C-terminal 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 / : / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / Laminin / Laminin / Coagulation Factor Xa inhibitory site / 6 Propeller / Neuraminidase / 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 / 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 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

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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

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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

1ijq

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

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