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Open data
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Basic information
Entry | Database: PDB / ID: 4ad7 | ||||||
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Title | Crystal structure of full-length N-glycosylated human glypican-1 | ||||||
![]() | GLYPICAN-1 | ||||||
![]() | MEMBRANE PROTEIN / PROTEOGLYCAN / GLYCOSAMINOGLYCANS / HEPARAN SULFATE / HELICAL BUNDLE / GLYCOPROTEIN / SUGAR BINDING PROTEIN | ||||||
Function / homology | ![]() positive regulation of skeletal muscle cell differentiation / regulation of protein localization to membrane / myelin assembly / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Schwann cell differentiation / A tetrasaccharide linker sequence is required for GAG synthesis ...positive regulation of skeletal muscle cell differentiation / regulation of protein localization to membrane / myelin assembly / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Schwann cell differentiation / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / negative regulation of fibroblast growth factor receptor signaling pathway / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / Signaling by ROBO receptors / RSV-host interactions / fibroblast growth factor binding / Respiratory syncytial virus (RSV) attachment and entry / side of membrane / Retinoid metabolism and transport / laminin binding / lysosomal lumen / extracellular matrix / Cell surface interactions at the vascular wall / Golgi lumen / cell migration / collagen-containing extracellular matrix / Attachment and Entry / endosome / membrane raft / copper ion binding / synapse / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Svensson, G. / Awad, W. / Mani, K. / Logan, D.T. | ||||||
![]() | ![]() Title: Crystal Structure of N-Glycosylated Human Glypican-1 Core Protein: Structure of Two Loops Evolutionarily Conserved in Vertebrate Glypican-1. Authors: Svensson, G. / Awad, W. / Hakansson, M. / Mani, K. / Logan, D.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 646.9 KB | Display | ![]() |
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PDB format | ![]() | 536 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4acrSC S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58785.254 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 24-529 Source method: isolated from a genetically manipulated source Details: N-GLYCOSYLATED AT RESIDUES 79 AND 116 / Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL HIS-TAG ADDED, GPI-ANCHOR REGION REMOVED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 8 Details: 12-14% PEG 6000, 0.1 M TRIS-HCL, 0.2 M CACL2, PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 1, 2011 / Details: HORIZONTALLY FOCUSING MIRROR |
Radiation | Monochromator: BENT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0397 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 49679 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 52.52 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.4 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ACR Resolution: 2.945→29.757 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 34.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.889 Å2 / ksol: 0.309 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.945→29.757 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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