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- PDB-4xhj: gHgL of Varicella-zoster virus in complex with human neutralizing... -

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Basic information

Entry
Database: PDB / ID: 4xhj
TitlegHgL of Varicella-zoster virus in complex with human neutralizing antibodies.
Components
  • (Envelope glycoprotein ...) x 2
  • Fab-RC heavy chain
  • Fab-RC light chain
KeywordsViral Protein/Immune System / complex / neutralization epitopes / Viral Protein-Immune System complex
Function / homology
Function and homology information


host cell endosome membrane / host cell Golgi apparatus / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Alphaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein L, N-terminal / Herpesvirus glycoprotein L, N-terminal domain superfamily / Herpesvirus glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain ...Alphaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein L, N-terminal / Herpesvirus glycoprotein L, N-terminal domain superfamily / Herpesvirus glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein H / Envelope glycoprotein L
Similarity search - Component
Biological speciesHuman herpesvirus 3 strain Oka vaccine
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.156 Å
AuthorsXing, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: A site of varicella-zoster virus vulnerability identified by structural studies of neutralizing antibodies bound to the glycoprotein complex gHgL.
Authors: Xing, Y. / Oliver, S.L. / Nguyen, T. / Ciferri, C. / Nandi, A. / Hickman, J. / Giovani, C. / Yang, E. / Palladino, G. / Grose, C. / Uematsu, Y. / Lilja, A.E. / Arvin, A.M. / Carfi, A.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Fab-RC light chain
D: Fab-RC heavy chain
E: Envelope glycoprotein H
F: Envelope glycoprotein L
G: Fab-RC light chain
H: Fab-RC heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,61716
Polymers323,6968
Non-polymers3,9218
Water00
1
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Fab-RC light chain
D: Fab-RC heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7888
Polymers161,8484
Non-polymers1,9404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-64 kcal/mol
Surface area53800 Å2
MethodPISA
2
E: Envelope glycoprotein H
F: Envelope glycoprotein L
G: Fab-RC light chain
H: Fab-RC heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,8298
Polymers161,8484
Non-polymers1,9814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14990 Å2
ΔGint-61 kcal/mol
Surface area53030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.001, 147.001, 198.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Envelope glycoprotein ... , 2 types, 4 molecules AEBF

#1: Protein Envelope glycoprotein H / gH / Glycoprotein III / GPIII


Mass: 92763.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 3 strain Oka vaccine / Gene: gH, ORF37 / Production host: Homo sapiens (human) / References: UniProt: Q775J3
#2: Protein Envelope glycoprotein L / gL


Mass: 15197.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 3 strain Oka vaccine / Gene: gL, ORF60 / Production host: Homo sapiens (human) / References: UniProt: Q9J3N1

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Antibody , 2 types, 4 molecules CGDH

#3: Antibody Fab-RC light chain


Mass: 23549.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Fab-RC heavy chain


Mass: 30338.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 4 types, 8 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 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.: 3 / Source method: obtained synthetically / 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

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 9% PEG 3350 and 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→200 Å / Num. obs: 71938 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M1C

3m1c


Resolution: 3.156→41.104 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 3630 5.05 %
Rwork0.2362 --
obs0.2383 71938 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.156→41.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19246 0 259 0 19505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420004
X-RAY DIFFRACTIONf_angle_d1.18127336
X-RAY DIFFRACTIONf_dihedral_angle_d14.157119
X-RAY DIFFRACTIONf_chiral_restr0.0643225
X-RAY DIFFRACTIONf_plane_restr0.0113442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1558-3.19730.37761140.30712547X-RAY DIFFRACTION95
3.1973-3.24110.35171270.30722584X-RAY DIFFRACTION100
3.2411-3.28740.34091460.3032625X-RAY DIFFRACTION100
3.2874-3.33640.40411230.30192649X-RAY DIFFRACTION100
3.3364-3.38850.34651360.28872614X-RAY DIFFRACTION100
3.3885-3.44410.34491480.28092601X-RAY DIFFRACTION100
3.4441-3.50340.32741420.2712660X-RAY DIFFRACTION100
3.5034-3.56710.33211550.26252557X-RAY DIFFRACTION100
3.5671-3.63570.32511350.26312651X-RAY DIFFRACTION100
3.6357-3.70980.32981420.25912602X-RAY DIFFRACTION100
3.7098-3.79040.32271280.26492632X-RAY DIFFRACTION100
3.7904-3.87860.33811530.25332651X-RAY DIFFRACTION100
3.8786-3.97550.27221470.25352612X-RAY DIFFRACTION100
3.9755-4.08290.33811440.25362629X-RAY DIFFRACTION100
4.0829-4.20290.2671360.22932625X-RAY DIFFRACTION100
4.2029-4.33840.25061460.22192633X-RAY DIFFRACTION100
4.3384-4.49330.22491460.20652622X-RAY DIFFRACTION100
4.4933-4.6730.23821520.20262612X-RAY DIFFRACTION100
4.673-4.88530.24941290.20212641X-RAY DIFFRACTION100
4.8853-5.14240.26441410.21352664X-RAY DIFFRACTION100
5.1424-5.46390.2781310.23772657X-RAY DIFFRACTION100
5.4639-5.88470.30741390.25862642X-RAY DIFFRACTION100
5.8847-6.47480.32031230.23922661X-RAY DIFFRACTION100
6.4748-7.4070.28951450.24622644X-RAY DIFFRACTION100
7.407-9.31410.25741310.20662663X-RAY DIFFRACTION100
9.3141-41.10740.2281710.22482630X-RAY DIFFRACTION99

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