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- PDB-5vod: Crystal structure of HCMV Pentamer in complex with neutralizing a... -

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Basic information

Entry
Database: PDB / ID: 5vod
TitleCrystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6
Components
  • (Envelope glycoprotein ...) x 5
  • Fab 9I6 heavy chain
  • Fab 9I6 light chain
KeywordsViral Protein/Immune System / HCMV / neutralizing epitope / immunogen / viral entry / Pentamer / vaccine / IMMUNE SYSTEM / Viral Protein-Immune System complex
Function / homology
Function and homology information


immunoglobulin complex / host cell endosome membrane / HCMV Late Events / HCMV Early Events / host cell Golgi apparatus / adaptive immune response / entry receptor-mediated virion attachment to host cell / immune response / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...immunoglobulin complex / host cell endosome membrane / HCMV Late Events / HCMV Early Events / host cell Golgi apparatus / adaptive immune response / entry receptor-mediated virion attachment to host cell / immune response / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular space / membrane / metal ion binding / plasma membrane
Similarity search - Function
Herpesvirus UL130, cytomegalovirus / HCMV glycoprotein pUL130 / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / 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 ...Herpesvirus UL130, cytomegalovirus / HCMV glycoprotein pUL130 / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / 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 / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein UL130 / Protein UL131A / Uncharacterized protein UL128 / Envelope glycoprotein L / Envelope glycoprotein H / Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesHuman cytomegalovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.9 Å
AuthorsMalito, E. / Chandramouli, S.
CitationJournal: Sci Immunol / Year: 2017
Title: Structural basis for potent antibody-mediated neutralization of human cytomegalovirus.
Authors: Chandramouli, S. / Malito, E. / Nguyen, T. / Luisi, K. / Donnarumma, D. / Xing, Y. / Norais, N. / Yu, D. / Carfi, A.
History
DepositionMay 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Envelope glycoprotein UL128
D: Envelope glycoprotein UL130
E: Envelope glycoprotein UL131A
H: Fab 9I6 heavy chain
L: Fab 9I6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,95313
Polymers233,9477
Non-polymers4,0066
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31360 Å2
ΔGint-121 kcal/mol
Surface area74800 Å2
2
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Envelope glycoprotein UL128
D: Envelope glycoprotein UL130
E: Envelope glycoprotein UL131A
H: Fab 9I6 heavy chain
L: Fab 9I6 light chain
hetero molecules

A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Envelope glycoprotein UL128
D: Envelope glycoprotein UL130
E: Envelope glycoprotein UL131A
H: Fab 9I6 heavy chain
L: Fab 9I6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,90626
Polymers467,89414
Non-polymers8,01112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area62940 Å2
ΔGint-218 kcal/mol
Surface area149370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.259, 208.820, 267.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Envelope glycoprotein ... , 5 types, 5 molecules ABCDE

#1: Protein Envelope glycoprotein H / gH


Mass: 82415.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Strain: Merlin / Gene: gH, UL75 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q6SW67
#2: Protein Envelope glycoprotein L / gL


Mass: 30846.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain 5508) / Strain: 5508 / Gene: gL, UL115 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q68674
#3: Protein Envelope glycoprotein UL128


Mass: 19777.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain AD169) / Strain: AD169 / Gene: UL128 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P16837
#4: Protein Envelope glycoprotein UL130


Mass: 28664.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain Merlin) / Strain: Merlin / Gene: UL130 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: F5HCP3
#5: Protein Envelope glycoprotein UL131A


Mass: 15011.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain Merlin) / Strain: Merlin / Gene: UL131A / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: F5HET4

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Antibody , 2 types, 2 molecules HL

#6: Antibody Fab 9I6 heavy chain


Mass: 30610.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B291
#7: Antibody Fab 9I6 light chain


Mass: 26621.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0

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Sugars , 3 types, 6 molecules

#8: 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.: 3
Source method: isolated from a genetically manipulated source
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
#9: 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
#10: 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.: 1
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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Details

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: 4.43 Å3/Da / Density % sol: 72.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 10% (wt/vol) PEG methyl ether 500 0.1 M MES pH 6.2 0.00001 M phenol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 5.9→45.71 Å / Num. obs: 11302 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 332.37 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.129 / Net I/σ(I): 8.6
Reflection shellResolution: 5.9→6.1 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3153 / CC1/2: 0.869 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VOB

5vob


Resolution: 5.9→45.71 Å / Cor.coef. Fo:Fc: 0.691 / Cor.coef. Fo:Fc free: 0.608 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.921
RfactorNum. reflection% reflectionSelection details
Rfree0.299 504 4.47 %RANDOM
Rwork0.258 ---
obs0.26 11268 100 %-
Displacement parametersBiso mean: 75.52 Å2
Baniso -1Baniso -2Baniso -3
1--114.4072 Å20 Å20 Å2
2--121.5964 Å20 Å2
3----7.1892 Å2
Refine analyzeLuzzati coordinate error obs: 0.91 Å
Refinement stepCycle: 1 / Resolution: 5.9→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13668 0 267 0 13935
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114364HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.319584HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6584SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes321HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2063HARMONIC5
X-RAY DIFFRACTIONt_it14364HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion3.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1947SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16510SEMIHARMONIC4
LS refinement shellResolution: 5.9→6.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 105 3.96 %
Rwork0.266 2548 -
all0.271 2653 -
obs--99.96 %

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