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- PDB-4acr: Crystal structure of N-glycosylated, C-terminally truncated human... -

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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


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 / heparan sulfate proteoglycan catabolic process / HS-GAG biosynthesis / negative regulation of fibroblast growth factor receptor signaling pathway / HS-GAG degradation / Signaling by ROBO receptors / fibroblast growth factor binding / laminin binding / Retinoid metabolism and transport / side of membrane / extracellular matrix / lysosomal lumen / Cell surface interactions at the vascular wall / Golgi lumen / cell migration / collagen-containing extracellular matrix / Attachment and Entry / endosome / copper ion binding / membrane raft / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
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

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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: 2.7 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

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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

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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

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