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- PDB-4hsi: Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507... -

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Basic information

Entry
Database: PDB / ID: 4hsi
TitleGlycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / viral fusion protein / viral envelope
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / PH-domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
MESO-ERYTHRITOL / Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.101 Å
AuthorsHeldwein, E.E.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Extensive Mutagenesis of the HSV-1 gB Ectodomain Reveals Remarkable Stability of Its Postfusion Form.
Authors: Vitu, E. / Sharma, S. / Stampfer, S.D. / Heldwein, E.E.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein B
B: Envelope glycoprotein B
C: Envelope glycoprotein B
D: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,35018
Polymers314,7884
Non-polymers2,56214
Water32418
1
A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,50115
Polymers236,0913
Non-polymers2,41012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area40040 Å2
ΔGint-205 kcal/mol
Surface area80130 Å2
MethodPISA
2
B: Envelope glycoprotein B
hetero molecules

B: Envelope glycoprotein B
hetero molecules

B: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,52512
Polymers236,0913
Non-polymers1,4349
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area38280 Å2
ΔGint-190 kcal/mol
Surface area81190 Å2
MethodPISA
3
C: Envelope glycoprotein B
hetero molecules

C: Envelope glycoprotein B
hetero molecules

C: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,50115
Polymers236,0913
Non-polymers2,41012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area39630 Å2
ΔGint-212 kcal/mol
Surface area81180 Å2
MethodPISA
4
D: Envelope glycoprotein B
hetero molecules

D: Envelope glycoprotein B
hetero molecules

D: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,52512
Polymers236,0913
Non-polymers1,4349
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area38550 Å2
ΔGint-200 kcal/mol
Surface area79530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.295, 117.295, 321.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Envelope glycoprotein B / gB / gB-1 / gB1


Mass: 78697.094 Da / Num. of mol.: 4 / Fragment: ectodomain / Mutation: A504P, R505G, Q507G, N511G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: KOS / Gene: gB, UL27 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06437

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Sugars , 2 types, 8 molecules

#2: 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: isolated from a genetically manipulated source
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
#3: 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.: 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

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Non-polymers , 3 types, 24 molecules

#4: Chemical ChemComp-MRY / MESO-ERYTHRITOL / Erythritol


Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→45.91 Å / Num. all: 89814 / Num. obs: 74374 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 52.48 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.25
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3 / Num. unique all: 7834 / % possible all: 87.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3NWA

3nwa


Resolution: 3.101→45.906 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 37.19 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 4373 5.88 %random
Rwork0.2052 ---
all0.2303 89814 --
obs0.2303 74374 82.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.101→45.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19475 0 160 18 19653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00920144
X-RAY DIFFRACTIONf_angle_d1.20527343
X-RAY DIFFRACTIONf_dihedral_angle_d17.5487403
X-RAY DIFFRACTIONf_chiral_restr0.0772979
X-RAY DIFFRACTIONf_plane_restr0.0053559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1667-3.21630.42166670.31552612X-RAY DIFFRACTION69
3.2163-3.2692000.31643413X-RAY DIFFRACTION88
3.2692-3.3258000.30293299X-RAY DIFFRACTION86
3.3258-3.38650.35871530.28763202X-RAY DIFFRACTION83
3.3865-3.45190.32234910.26392854X-RAY DIFFRACTION74
3.4519-3.5226000.2693269X-RAY DIFFRACTION86
3.5226-3.5995000.24993261X-RAY DIFFRACTION85
3.5995-3.68370.29883550.25012957X-RAY DIFFRACTION76
3.6837-3.77620.28622880.2332964X-RAY DIFFRACTION77
3.7762-3.8789000.22383220X-RAY DIFFRACTION84
3.8789-3.9937000.21373243X-RAY DIFFRACTION84
3.9937-4.12350.28664800.20592715X-RAY DIFFRACTION71
4.1235-4.27190.26311560.19113011X-RAY DIFFRACTION79
4.2719-4.4443000.17393210X-RAY DIFFRACTION83
4.4443-4.6484000.163131X-RAY DIFFRACTION82
4.6484-4.89610.23156120.17682554X-RAY DIFFRACTION66
4.8961-5.20670.013410.17823062X-RAY DIFFRACTION80
5.2067-5.615000.20623054X-RAY DIFFRACTION79
5.615-6.1916000.23443009X-RAY DIFFRACTION78
6.1916-7.11420.27115710.22352362X-RAY DIFFRACTION62

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