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- PDB-1l2g: Structure of a C-terminally truncated form of glycoprotein D from... -

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Basic information

Entry
Database: PDB / ID: 1l2g
TitleStructure of a C-terminally truncated form of glycoprotein D from HSV-1
ComponentsGlycoprotein D
KeywordsVIRAL PROTEIN / Ig fold / viral envelope glycoprotein
Function / homology
Function and homology information


host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / viral envelope / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Distorted Sandwich / Immunoglobulin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein D
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsCarfi, A. / Willis, S.H. / Whitbeck, J.C. / Krummenacher, C. / Cohen, G.H. / Eisenberg, R.J. / Wiley, D.C.
Citation
Journal: Mol.Cell / Year: 2001
Title: Herpes simplex virus glycoprotein D bound to the human receptor HveA.
Authors: Carfi, A. / Willis, S.H. / Whitbeck, J.C. / Krummenacher, C. / Cohen, G.H. / Eisenberg, R.J. / Wiley, D.C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: HERPES SIMPLEX VIRUS-1 ENTRY INTO CELLS MEDIATED BY A NOVEL MEMBER OF THE TNF/NGF RECEPTOR FAMILY
Authors: MONTGOMERY, R.I. / WARNER, M.S. / LUM, B.J. / SPEAR, P.G.
History
DepositionFeb 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 16, 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
Remark 300BIOMOLECULE: 1, 2, 3, 4 ACCORDING TO THE AUTHOR, THIS C-TERMINALLY TRUNCATED GD MOLECULE (RESIDUES ...BIOMOLECULE: 1, 2, 3, 4 ACCORDING TO THE AUTHOR, THIS C-TERMINALLY TRUNCATED GD MOLECULE (RESIDUES 1 TO 285) IS MONOMERIC IN SOLUTION, BUT FORMED DIMERS IN THE CRYSTAL. THIS ENTRY CONTAINS TWO DIMERS, AN AB DIMER CONSISTING OF CHAINS A AND B, AND A CD DIMER CONSISTING OF CHAINS C AND D.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein D
B: Glycoprotein D
D: Glycoprotein D
C: Glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2348
Polymers127,3494
Non-polymers8854
Water0
1
A: Glycoprotein D
B: Glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1174
Polymers63,6742
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-2 kcal/mol
Surface area23300 Å2
MethodPISA
2
D: Glycoprotein D
C: Glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1174
Polymers63,6742
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-2 kcal/mol
Surface area23340 Å2
MethodPISA
3
A: Glycoprotein D
B: Glycoprotein D
hetero molecules

A: Glycoprotein D
B: Glycoprotein D
hetero molecules

A: Glycoprotein D
B: Glycoprotein D
hetero molecules

A: Glycoprotein D
B: Glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,46716
Polymers254,6978
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area20900 Å2
ΔGint-33 kcal/mol
Surface area84210 Å2
MethodPISA
4
D: Glycoprotein D
C: Glycoprotein D
hetero molecules

D: Glycoprotein D
C: Glycoprotein D
hetero molecules

D: Glycoprotein D
C: Glycoprotein D
hetero molecules

D: Glycoprotein D
C: Glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,46716
Polymers254,6978
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area20720 Å2
ΔGint-33 kcal/mol
Surface area84460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.416, 131.416, 83.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Number of models2

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Components

#1: Protein
Glycoprotein D


Mass: 31837.168 Da / Num. of mol.: 4 / Fragment: Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Plasmid: PFASTBAC-DUAL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P57083
#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 / N-Acetylglucosamine


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

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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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Ammonium Sulfate, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 10, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 29319 / % possible obs: 87.1 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.076 / Net I/σ(I): 11
Reflection shellResolution: 2.85→2.95 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.23 / % possible all: 67.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
CNS1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JMA

1jma


Resolution: 2.85→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: THE CRYSTALS ARE MEROHEDRALLY TWINNED. THE TWINNING OPERATION IS A 2 FOLD ROTATION PARALLEL TO THE A AXIS. THE TWO BLOCKS ARE REPRESENTED IN THIS ENTRY BY TWO MODELS (MODEL 1 AND MODEL 2) ...Details: THE CRYSTALS ARE MEROHEDRALLY TWINNED. THE TWINNING OPERATION IS A 2 FOLD ROTATION PARALLEL TO THE A AXIS. THE TWO BLOCKS ARE REPRESENTED IN THIS ENTRY BY TWO MODELS (MODEL 1 AND MODEL 2) CONTAINING 4 CHAINS (ABCD) EACH. MOLECULES ABCD IN MODEL 1 ARE RELATED BY A 2 FOLD ROTATION AXIS (TWIN OPERATION) TO MOLECULES ABCD OF MODEL 2. NO DETWINNING OF THE DATA WAS ATTEMPTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1425 -RANDOM
Rwork0.278 ---
all0.288 29319 --
obs0.283 29042 88 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.761 Å20 Å20 Å2
2---7.481 Å20 Å2
3---15.242 Å2
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7632 0 56 0 7688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.674
LS refinement shellResolution: 2.85→2.98 Å
RfactorNum. reflection% reflection
Rfree0.398 156 -
Rwork0.359 --
obs-2819 0.71 %

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