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- PDB-7lyv: Crystal structure of the HCMV pentamer-specific antibody 1-103 -

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Basic information

Entry
Database: PDB / ID: 7lyv
TitleCrystal structure of the HCMV pentamer-specific antibody 1-103
Components
  • 1-103 Fab Heavy Chain
  • 1-103 Fab Light Chain
KeywordsIMMUNE SYSTEM / Fab / HCMV Pentamer / antibody / cytomegalovirus
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWrapp, D. / Jones, H.G. / McLellan, J.S.
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for HCMV Pentamer recognition by neuropilin 2 and neutralizing antibodies.
Authors: Daniel Wrapp / Xiaohua Ye / Zhiqiang Ku / Hang Su / Harrison G Jones / Nianshuang Wang / Akaash K Mishra / Daniel C Freed / Fengsheng Li / Aimin Tang / Leike Li / Dabbu Kumar Jaijyan / Hua ...Authors: Daniel Wrapp / Xiaohua Ye / Zhiqiang Ku / Hang Su / Harrison G Jones / Nianshuang Wang / Akaash K Mishra / Daniel C Freed / Fengsheng Li / Aimin Tang / Leike Li / Dabbu Kumar Jaijyan / Hua Zhu / Dai Wang / Tong-Ming Fu / Ningyan Zhang / Zhiqiang An / Jason S McLellan /
Abstract: Human cytomegalovirus (HCMV) encodes multiple surface glycoprotein complexes to infect a variety of cell types. The HCMV Pentamer, composed of gH, gL, UL128, UL130, and UL131A, enhances entry into ...Human cytomegalovirus (HCMV) encodes multiple surface glycoprotein complexes to infect a variety of cell types. The HCMV Pentamer, composed of gH, gL, UL128, UL130, and UL131A, enhances entry into epithelial, endothelial, and myeloid cells by interacting with the cell surface receptor neuropilin 2 (NRP2). Despite the critical nature of this interaction, the molecular determinants that govern NRP2 recognition remain unclear. Here, we describe the cryo-EM structure of NRP2 bound to Pentamer. The high-affinity interaction between these proteins is calcium dependent and differs from the canonical carboxyl-terminal arginine (CendR) binding that NRP2 typically uses. We also determine the structures of four neutralizing human antibodies bound to the HCMV Pentamer to define susceptible epitopes. Two of these antibodies compete with NRP2 binding, but the two most potent antibodies recognize a previously unidentified epitope that does not overlap the NRP2-binding site. Collectively, these findings provide a structural basis for HCMV tropism and antibody-mediated neutralization.
History
DepositionMar 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 1-103 Fab Heavy Chain
L: 1-103 Fab Light Chain
C: 1-103 Fab Heavy Chain
D: 1-103 Fab Light Chain
A: 1-103 Fab Heavy Chain
B: 1-103 Fab Light Chain
E: 1-103 Fab Heavy Chain
F: 1-103 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)190,0078
Polymers190,0078
Non-polymers00
Water29,3101627
1
H: 1-103 Fab Heavy Chain
L: 1-103 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,5022
Polymers47,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-24 kcal/mol
Surface area18900 Å2
MethodPISA
2
C: 1-103 Fab Heavy Chain
D: 1-103 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,5022
Polymers47,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-26 kcal/mol
Surface area18880 Å2
MethodPISA
3
A: 1-103 Fab Heavy Chain
B: 1-103 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,5022
Polymers47,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area18760 Å2
MethodPISA
4
E: 1-103 Fab Heavy Chain
F: 1-103 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,5022
Polymers47,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-26 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.389, 105.240, 102.730
Angle α, β, γ (deg.)90.000, 91.370, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11L-489-

HOH

21A-500-

HOH

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Components

#1: Antibody
1-103 Fab Heavy Chain


Mass: 24662.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
1-103 Fab Light Chain


Mass: 22839.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1627 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2.1 M sodium formate, 25% PEG 3350, 0.1 M sodium acetate pH 4.5, 0.1 M calcium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→52.62 Å / Num. obs: 143460 / % possible obs: 89.88 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 5.9
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 14384 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XZC

2xzc


Resolution: 1.9→46.83 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2173 --
Rwork0.191 --
obs-143434 89.88 %
Displacement parametersBiso max: 74.22 Å2 / Biso mean: 29.8376 Å2 / Biso min: 9.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12781 0 0 1628 14409

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