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- PDB-4bwe: Crystal structure of C-terminally truncated glypican-1 after cont... -

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Basic information

Entry
Database: PDB / ID: 4bwe
TitleCrystal structure of C-terminally truncated glypican-1 after controlled dehydration to 86 percent relative humidity
ComponentsGlypican-1
KeywordsMEMBRANE PROTEIN / PROTEOGLYCAN / GLYCOSAMINOGLYCANS / HEPARAN SULFATE / GLYCOPROTEIN / HELICAL BUNDLE
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: 2.46 Å
AuthorsAwad, W. / Svensson Birkedal, G. / Thunnissen, M.M.G.M. / Mani, K. / Logan, D.T.
Citation
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.
#1: 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
DepositionJul 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Atomic model / Derived calculations / Other
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 28, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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.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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: 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 1.6Nov 20, 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)216,10517
Polymers214,8594
Non-polymers1,24613
Water6,792377
1
A: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0164
Polymers53,7151
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0164
Polymers53,7151
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0565
Polymers53,7151
Non-polymers3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glypican-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0164
Polymers53,7151
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.230, 166.720, 139.090
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number4
Space group name H-MP1211

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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
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.: 377 / 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: 2.53 Å3/Da / Density % sol: 51.4 % / Description: NONE
Crystal growpH: 8 / Details: 13 % PEG 6000, 0.1 M TRIS-HCL PH 8 & 0.2 M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→29.48 Å / Num. obs: 75752 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ACR

4acr


Resolution: 2.46→29.476 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 32.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 3805 5 %
Rwork0.2287 --
obs0.2313 75695 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12801 0 65 377 13243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413209
X-RAY DIFFRACTIONf_angle_d0.8917863
X-RAY DIFFRACTIONf_dihedral_angle_d14.1714937
X-RAY DIFFRACTIONf_chiral_restr0.0341993
X-RAY DIFFRACTIONf_plane_restr0.0042351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.49110.37181320.322714X-RAY DIFFRACTION97
2.4911-2.52390.37321210.31882588X-RAY DIFFRACTION97
2.5239-2.55840.34991390.30582655X-RAY DIFFRACTION97
2.5584-2.59490.2871520.29642639X-RAY DIFFRACTION97
2.5949-2.63360.3611220.29952713X-RAY DIFFRACTION97
2.6336-2.67480.39451450.29412621X-RAY DIFFRACTION97
2.6748-2.71860.29291260.29062623X-RAY DIFFRACTION97
2.7186-2.76540.30151310.2762723X-RAY DIFFRACTION98
2.7654-2.81570.31881420.27692652X-RAY DIFFRACTION98
2.8157-2.86980.32361400.26922666X-RAY DIFFRACTION98
2.8698-2.92830.33481580.26832690X-RAY DIFFRACTION98
2.9283-2.99190.33811300.262712X-RAY DIFFRACTION99
2.9919-3.06150.28641630.25362608X-RAY DIFFRACTION98
3.0615-3.13790.27841540.23662764X-RAY DIFFRACTION99
3.1379-3.22270.29691500.24092632X-RAY DIFFRACTION99
3.2227-3.31740.32321480.23822719X-RAY DIFFRACTION99
3.3174-3.42430.29521480.22872688X-RAY DIFFRACTION99
3.4243-3.54650.25891330.22542675X-RAY DIFFRACTION98
3.5465-3.68830.32551180.23432577X-RAY DIFFRACTION93
3.6883-3.85580.26241380.21152630X-RAY DIFFRACTION96
3.8558-4.05860.25541370.20952586X-RAY DIFFRACTION95
4.0586-4.31210.23061630.1912703X-RAY DIFFRACTION98
4.3121-4.64390.2031300.17012692X-RAY DIFFRACTION98
4.6439-5.1090.24061590.17992645X-RAY DIFFRACTION98
5.109-5.84330.2621470.20812722X-RAY DIFFRACTION98
5.8433-7.34310.30291530.23612640X-RAY DIFFRACTION97
7.3431-29.47770.2211260.18082613X-RAY DIFFRACTION93
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)
12.5063-1.44330.29382.6156-0.39790.5510.12420.1671-0.1344-0.129-0.1415-0.2040.07090.06560.04810.3840.01390.08350.28980.06330.32343.0881.2397-7.8449
23.28112.935-0.28244.2071-0.49130.7012-0.008-0.05590.2477-0.0812-0.0168-0.1877-0.17360.10690.02130.4178-0.03770.04490.36730.02910.34815.79615.041421.9083
32.1584-1.43250.17053.2499-0.26120.71510.12750.1282-0.0721-0.3475-0.1082-0.26770.0688-0.02120.00140.22570.0180.05860.2448-0.01610.369725.903213.658361.4227
42.47741.54730.73882.01910.51440.98230.1599-0.1837-0.31280.096-0.1230.10770.1255-0.16980.00710.14780.03960.0030.1969-0.02860.279438.793118.115590.8663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN D
2X-RAY DIFFRACTION2CHAIN C
3X-RAY DIFFRACTION3CHAIN B
4X-RAY DIFFRACTION4CHAIN A

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