[English] 日本語
Yorodumi
- PDB-4acr: Crystal structure of N-glycosylated, C-terminally truncated human... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4acr
TitleCrystal structure of N-glycosylated, C-terminally truncated human glypican-1
ComponentsGLYPICAN-1
KeywordsMEMBRANE PROTEIN / PROTEOGLYCAN / GLYCOSAMINOGLYCANS / HEPARAN SULFATE / HELICAL BUNDLE / GLYCOPROTEIN
Function / homology
Function and homology information


regulation of protein localization to membrane / positive regulation of skeletal muscle cell differentiation / 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 / Glycosaminoglycan-protein linkage region biosynthesis ...regulation of protein localization to membrane / positive regulation of skeletal muscle cell differentiation / 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 / Glycosaminoglycan-protein linkage region biosynthesis / 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 / Retinoid metabolism and transport / side of membrane / laminin binding / extracellular matrix / lysosomal lumen / Cell surface interactions at the vascular wall / Golgi lumen / cell migration / : / 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
Glypican, conserved site / Glypicans signature. / Glypican / Glypican
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsSvensson, G. / Awad, W. / Mani, K. / Logan, D.T.
CitationJournal: J.Biol.Chem. / Year: 2012
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
DepositionDec 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYPICAN-1
B: GLYPICAN-1
C: GLYPICAN-1
D: GLYPICAN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,18710
Polymers214,8594
Non-polymers1,3276
Water4,360242
1
A: GLYPICAN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9362
Polymers53,7151
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYPICAN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1573
Polymers53,7151
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLYPICAN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9362
Polymers53,7151
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GLYPICAN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1573
Polymers53,7151
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.170, 168.630, 147.760
Angle α, β, γ (deg.)90.00, 94.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9998, -0.007582, -0.01765), (-0.002682, -0.9649, 0.2626), (-0.01902, -0.2625, -0.9648)15.71, -23.5, 304.1
2given(0.9997, 0.02267, 0.01004), (-0.02286, 0.9996, 0.01898), (-0.009609, -0.0192, 0.9998)13.56, 11.75, -71.23
3given(0.9978, -0.06051, -0.02649), (-0.05092, -0.9601, 0.2751), (-0.04208, -0.2731, -0.9611)33.19, -10.92, 232.4

-
Components

#1: Protein
GLYPICAN-1 / SECRETED GLYPICAN-1


Mass: 53714.855 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 24-479
Source method: isolated from a genetically manipulated source
Details: N-GLYCOSYLATED AT RESIDUES 79 AND 116 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCEP4 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P35052
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-ACETYLGLUCOSAMINE (NAG): N-GLYCOSYLATION OF RESIDUES A116, B79, B116, C116, D79 AND D116
Sequence detailsN-TERMINAL HIS-TAG, C-TERMINAL HEPARAN SULFATE ATTACHMENT AND GPI-ANCHOR REGIONS REMOVED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8
Details: 12-14% PEG 6000, 0.1 M TRIS-HCL, 0.2 M CACL2, PH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0397
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2011 / Details: HORIZONTALLY FOCUSING MIRROR
RadiationMonochromator: BENT SI(111) CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0397 Å / Relative weight: 1
ReflectionResolution: 2.49→30 Å / Num. obs: 79825 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 45.95 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 2.49→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.4 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.55→29.714 Å / SU ML: 0.76 / σ(F): 0 / Phase error: 34.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.292 3753 5 %
Rwork0.2509 --
obs0.253 74535 99.66 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.519 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.306 Å20 Å2-2.7859 Å2
2---10.4554 Å20 Å2
3---18.7615 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12486 0 84 242 12812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312826
X-RAY DIFFRACTIONf_angle_d0.71717309
X-RAY DIFFRACTIONf_dihedral_angle_d13.6434819
X-RAY DIFFRACTIONf_chiral_restr0.0531921
X-RAY DIFFRACTIONf_plane_restr0.0032272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5499-2.58220.37651480.33972565X-RAY DIFFRACTION99
2.5822-2.61610.3781400.32442676X-RAY DIFFRACTION99
2.6161-2.65190.39071170.32782578X-RAY DIFFRACTION100
2.6519-2.68980.4151130.33862617X-RAY DIFFRACTION100
2.6898-2.72990.38431400.31362627X-RAY DIFFRACTION100
2.7299-2.77250.38711490.31362641X-RAY DIFFRACTION100
2.7725-2.8180.31161390.29582561X-RAY DIFFRACTION99
2.818-2.86650.34551350.28532601X-RAY DIFFRACTION100
2.8665-2.91860.28431350.25642664X-RAY DIFFRACTION100
2.9186-2.97470.33161490.26482623X-RAY DIFFRACTION100
2.9747-3.03530.3691300.27072556X-RAY DIFFRACTION100
3.0353-3.10130.29671200.27672663X-RAY DIFFRACTION100
3.1013-3.17330.28721530.27032634X-RAY DIFFRACTION100
3.1733-3.25260.31291310.27022575X-RAY DIFFRACTION100
3.2526-3.34040.31981420.27152655X-RAY DIFFRACTION100
3.3404-3.43860.33471530.25742622X-RAY DIFFRACTION100
3.4386-3.54940.25861340.25612599X-RAY DIFFRACTION100
3.5494-3.6760.29441380.25252642X-RAY DIFFRACTION100
3.676-3.82290.281420.25652609X-RAY DIFFRACTION100
3.8229-3.99650.32311310.24022655X-RAY DIFFRACTION100
3.9965-4.20670.27161430.23082625X-RAY DIFFRACTION100
4.2067-4.46940.26541660.22162590X-RAY DIFFRACTION100
4.4694-4.81320.27971520.20152650X-RAY DIFFRACTION100
4.8132-5.29510.25461540.21742630X-RAY DIFFRACTION100
5.2951-6.05570.30191400.25062632X-RAY DIFFRACTION100
6.0557-7.60830.31811240.2562653X-RAY DIFFRACTION100
7.6083-29.71610.19481350.21462639X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.74871.807-0.0432.5324-0.08961.27440.1656-0.2789-0.02090.1993-0.1813-0.08340.01930.06290.01440.1281-0.0643-0.04130.31120.00330.53123.76543.4599169.6083
21.3878-0.5540.30452.0482-0.53810.79490.0881-0.0347-0.1775-0.0672-0.0959-0.13460.10840.04860.0407-0.21430.08750.029-0.0485-0.00540.22615.68592.3202138.6024
32.74111.61340.45911.8560.45860.74050.0221-0.20790.06560.0251-0.09060.01480.0326-0.05680.0105-0.1889-0.09430.02880.0612-0.08820.412410.28884.090296.5238
42.1409-1.48440.05052.5523-0.33430.41350.22490.14990.004-0.2689-0.1673-0.13210.0590.00370.0309-0.06770.15780.0584-0.07410.09320.4141-1.7222-0.733265.7536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more