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- PDB-2c3a: Structure of unliganded HSV gD reveals a mechanism for receptor- ... -

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Basic information

Entry
Database: PDB / ID: 2c3a
TitleStructure of unliganded HSV gD reveals a mechanism for receptor- mediated activation of virus entry
ComponentsGLYCOPROTEIN D
KeywordsVIRAL PROTEIN / VIRUS / HERPES SIMPLEX VIRUS / HSV-1 / GLYCOPROTEIN D
Function / homology
Function and homology information


host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / viral envelope / symbiont entry into host cell / virion membrane / metal ion binding / membrane
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: 2.5 Å
AuthorsKrummenacher, C. / Supekar, V.M. / Whitbeck, J.C. / Lazear, E. / Connolly, S.A. / Eisenberg, R.J. / Cohen, G.H. / Wiley, D.C. / Carfi, A.
CitationJournal: Embo J. / Year: 2005
Title: Structure of Unliganded Hsv Gd Reveals a Mechanism for Receptor-Mediated Activation of Virus Entry.
Authors: Krummenacher, C. / Supekar, V.M. / Whitbeck, J.C. / Lazear, E. / Connolly, S.A. / Eisenberg, R.J. / Cohen, G.H. / Wiley, D.C. / Carfi, A.
History
DepositionOct 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,77913
Polymers63,4862
Non-polymers1,29311
Water95553
1
A: GLYCOPROTEIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2684
Polymers31,7431
Non-polymers5253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLYCOPROTEIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5119
Polymers31,7431
Non-polymers7678
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.629, 79.105, 123.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 100 - 200 / Label seq-ID: 79 - 179

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.96045, 0.27667, 0.03155), (0.2775, -0.96039, -0.02563), (0.02321, 0.03337, -0.99917)
Vector: -10.02013, 73.80945, -3.41714)

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein GLYCOPROTEIN D


Mass: 31743.059 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-ACETYL-D-GLUCOSAMINE LINKED TO ASN94 FOR BOTH CHAINS A AND B
Source: (gene. exp.) HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
Strain: PATTON / Plasmid: PDL485 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P57083
#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

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Non-polymers , 4 types, 62 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 62 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 327 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, VAL 62 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 327 TO CYS ENGINEERED RESIDUE IN CHAIN B, VAL 62 TO CYS ENGINEERED RESIDUE IN CHAIN B, ALA 327 TO CYS
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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.6 / Details: 100MM NA ACETATE PH 4.6, 10MM ZNCL2, 24% PEG &K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23602 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.07 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L2G

1l2g


Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.386 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FIRST 22 RESIDUES DISORDERED FOR BOTH CHAINS A,B. RESIDUES 256-267 DISORDERED FOR BOTH CHAINS A,B
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1212 5.2 %RANDOM
Rwork0.226 ---
obs0.228 22271 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 65 53 4185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224279
X-RAY DIFFRACTIONr_bond_other_d0.0020.023833
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9795878
X-RAY DIFFRACTIONr_angle_other_deg0.93138929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8065519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024667
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02819
X-RAY DIFFRACTIONr_nbd_refined0.2060.2788
X-RAY DIFFRACTIONr_nbd_other0.2350.24271
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.22539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0070.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9031.52644
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65524317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.01131635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4124.51561
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
593tight positional0.040.05
931medium positional0.260.5
593tight thermal0.170.5
931medium thermal0.732
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.431 81
Rwork0.278 1565

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