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- PDB-5c6t: Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab -

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Basic information

Entry
Database: PDB / ID: 5c6t
TitleCrystal structure of HCMV glycoprotein B in complex with 1G2 Fab
Components
  • 1G2 Fab heavy chain
  • 1G2 Fab light chain
  • Envelope glycoprotein B
KeywordsViral Protein/Immue System / Cytomegalovirus / glycoprotein B / gB / 1G2 / complex / Viral Protein-Immue System complex
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
Similarity search - Function
PH-domain like - #100 / Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain ...PH-domain like - #100 / Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / PH-domain like / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman cytomegalovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsChandramouli, S. / Ciferri, C. / Settembre, E.C. / Carfi, A.
CitationJournal: Nat Commun / Year: 2015
Title: Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody.
Authors: Chandramouli, S. / Ciferri, C. / Nikitin, P.A. / Calo, S. / Gerrein, R. / Balabanis, K. / Monroe, J. / Hebner, C. / Lilja, A.E. / Settembre, E.C. / Carfi, A.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
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 / diffrn_radiation_wavelength / 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_struct_conn_angle / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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
H: 1G2 Fab heavy chain
L: 1G2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,40813
Polymers121,1903
Non-polymers2,21810
Water00
1
A: Envelope glycoprotein B
H: 1G2 Fab heavy chain
L: 1G2 Fab light chain
hetero molecules

A: Envelope glycoprotein B
H: 1G2 Fab heavy chain
L: 1G2 Fab light chain
hetero molecules

A: Envelope glycoprotein B
H: 1G2 Fab heavy chain
L: 1G2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,22439
Polymers363,5699
Non-polymers6,65530
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area49740 Å2
ΔGint-138 kcal/mol
Surface area108570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.486, 176.486, 176.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1011-

MG

Detailsgel filtration, negative-stain electron microscopy

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody 1G2 Fab heavy chain


Mass: 25302.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
#3: Antibody 1G2 Fab light chain


Mass: 22853.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 2 molecules A

#1: Protein Envelope glycoprotein B / gB


Mass: 73034.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Strain: Towne / Gene: gB, UL55 / Cell line (production host): HEK293S GnTI-/- / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P13201
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Sugars , 2 types, 9 molecules

#4: 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
#5: 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.: 8
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

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.46 % / Description: Blunt pyramidal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 40mM MMT pH 9; 8% PEG8K; 0.1M NaCl; 20% glycerol / PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 22423 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 16.4
Reflection shellResolution: 3.55→3.74 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUM

2gum


Resolution: 3.6→19.983 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 1072 5.02 %
Rwork0.2116 --
obs0.2141 21341 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6267 0 141 0 6408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056581
X-RAY DIFFRACTIONf_angle_d1.1478930
X-RAY DIFFRACTIONf_dihedral_angle_d17.1452344
X-RAY DIFFRACTIONf_chiral_restr0.0471005
X-RAY DIFFRACTIONf_plane_restr0.0041135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6003-3.76310.32241220.26332508X-RAY DIFFRACTION100
3.7631-3.960.31561310.23642500X-RAY DIFFRACTION100
3.96-4.2060.27071170.20842548X-RAY DIFFRACTION100
4.206-4.52720.24331510.19022486X-RAY DIFFRACTION100
4.5272-4.97640.24021370.17952514X-RAY DIFFRACTION100
4.9764-5.6820.24411400.20352547X-RAY DIFFRACTION100
5.682-7.10490.32871260.24372549X-RAY DIFFRACTION100
7.1049-19.98340.23371480.20712617X-RAY DIFFRACTION100

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