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Open data
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Basic information
Entry | Database: PDB / ID: 1gl4 | ||||||
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Title | Nidogen-1 G2/Perlecan IG3 Complex | ||||||
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![]() | BASEMENT MEMBRANE / IMMUNOGLOBULIN-LIKE DOMAIN / EXTRACELLULAR MATRIX / PROTEOGLYCAN / HEPARAN SULFATE | ||||||
Function / homology | ![]() A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Non-integrin membrane-ECM interactions / Laminin interactions / regulation of basement membrane organization / Retinoid metabolism and transport / ECM proteoglycans / : / glomerular basement membrane development ...A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Non-integrin membrane-ECM interactions / Laminin interactions / regulation of basement membrane organization / Retinoid metabolism and transport / ECM proteoglycans / : / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / : / Degradation of the extracellular matrix / embryonic skeletal system morphogenesis / Integrin cell surface interactions / cartilage development involved in endochondral bone morphogenesis / Wnt receptor activity / tissue development / Wnt-protein binding / endochondral ossification / protein complex involved in cell-matrix adhesion / negative regulation of amyloid fibril formation / cardiac muscle tissue development / extracellular matrix binding / positive regulation of cell-substrate adhesion / proteoglycan binding / positive regulation of muscle cell differentiation / positive regulation of cell adhesion / basement membrane / canonical Wnt signaling pathway / chondrocyte differentiation / collagen binding / extracellular matrix organization / cell-matrix adhesion / extracellular matrix / receptor-mediated endocytosis / cell periphery / animal organ morphogenesis / protein localization / brain development / Golgi lumen / angiogenesis / collagen-containing extracellular matrix / protease binding / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kvansakul, M. / Hopf, M. / Ries, A. / Timpl, R. / Hohenester, E. | ||||||
![]() | ![]() 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: ![]() 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 |
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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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 65.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.9 KB | Display | ![]() |
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Full document | ![]() | 455.9 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h4uS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 31350.930 Da / Num. of mol.: 1 / Fragment: G2 RESIDUES 385-665 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | 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.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-EPE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: QUANTUM4 / Detector: CCD / Date: Nov 6, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 1H4U Resolution: 2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å / Total num. of bins used: 50
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Xplor file |
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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 |