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- PDB-4ywt: Crystal structure of full-length glypican-1 core protein after co... -

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Basic information

Entry
Database: PDB / ID: 4ywt
TitleCrystal structure of full-length glypican-1 core protein after controlled crystal dehydration to 87% relative humidity
ComponentsGlypican-1
KeywordsMEMBRANE PROTEIN / glypican-1 / diffraction quality / controlled dehydration / HC1b
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 / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsAwad, W. / Mani, K. / Logan, D.T.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Structural Aspects of N-Glycosylations and the C-terminal Region in Human Glypican-1.
Authors: Awad, W. / Adamczyk, B. / Ornros, J. / Karlsson, N.G. / Mani, K. / Logan, D.T.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration.
Authors: Awad, W. / Svensson Birkedal, G. / Thunnissen, M.M. / Mani, K. / Logan, D.T.
#2: Journal: 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
DepositionMar 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_symmetry / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 13, 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: Glypican-1
B: Glypican-1
C: Glypican-1
D: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,27317
Polymers234,0284
Non-polymers1,24613
Water5,116284
1
A: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8084
Polymers58,5071
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8084
Polymers58,5071
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8485
Polymers58,5071
Non-polymers3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8084
Polymers58,5071
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.780, 166.590, 137.700
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glypican-1


Mass: 58506.973 Da / Num. of mol.: 4 / Fragment: UNP residues 24-527 / Mutation: S486A, S488A and S490A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPC1 / 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.: 4
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000, Tris-HCl and CaCl2 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2014
RadiationMonochromator: double crystal, Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→43.22 Å / Num. obs: 82475 / % possible obs: 97.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.1076 / Net I/σ(I): 7.44
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.62 / % possible all: 97.11

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bwe

4bwe


Resolution: 2.38→43.223 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2728 1981 2.4 %
Rwork0.239 --
obs0.2398 82387 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→43.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12704 0 65 284 13053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413139
X-RAY DIFFRACTIONf_angle_d0.85617763
X-RAY DIFFRACTIONf_dihedral_angle_d14.9654775
X-RAY DIFFRACTIONf_chiral_restr0.0462019
X-RAY DIFFRACTIONf_plane_restr0.0032335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.43950.32431360.33835731X-RAY DIFFRACTION98
2.4395-2.50550.34941460.32795730X-RAY DIFFRACTION98
2.5055-2.57920.29481350.30865752X-RAY DIFFRACTION98
2.5792-2.66240.38991400.30435707X-RAY DIFFRACTION98
2.6624-2.75760.32371410.29625736X-RAY DIFFRACTION97
2.7576-2.8680.31421430.29155786X-RAY DIFFRACTION100
2.868-2.99850.31931420.27545703X-RAY DIFFRACTION98
2.9985-3.15650.32331420.27015809X-RAY DIFFRACTION98
3.1565-3.35420.291400.25745771X-RAY DIFFRACTION98
3.3542-3.6130.28471470.23745729X-RAY DIFFRACTION98
3.613-3.97640.25021350.21035680X-RAY DIFFRACTION97
3.9764-4.55130.25111430.19225792X-RAY DIFFRACTION98
4.5513-5.7320.21621450.20235801X-RAY DIFFRACTION98
5.732-43.23020.22021460.1965679X-RAY DIFFRACTION95
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)
12.09451.19820.40691.38780.26020.71750.1028-0.19-0.12680.0482-0.07070.03960.0916-0.0515-0.05150.1120.0330.07760.1713-0.03770.61539.375318.430290.4874
21.6448-0.92560.18291.6361-0.04620.55670.10490.1084-0.0128-0.1537-0.0833-0.13980.04410.00380.00280.16350.03880.07370.14770.02510.77327.206513.511461.0112
31.36331.0232-0.03781.7378-0.13540.63720.01540.04090.09850.00840.0173-0.0756-0.08730.0822-0.0640.3499-0.02950.05740.46010.08350.623816.21015.886821.9903
41.5457-1.23930.45651.5443-0.44530.6130.13590.1363-0.1363-0.1607-0.0938-0.12630.07170.0214-0.04020.30930.03070.09110.45920.09370.62994.19331.5994-7.6191
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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