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- PDB-8too: Crystal structure of Epstein-Barr virus gp42 in complex with anti... -

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Basic information

Entry
Database: PDB / ID: 8too
TitleCrystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12
Components
  • 4C12 heavy chain
  • 4C12 light chain
  • Glycoprotein 42
KeywordsIMMUNE SYSTEM / Viral Protein / Antibody
Function / homologyC-type lectin-like/link domain superfamily / C-type lectin fold / host cell membrane / carbohydrate binding / virion membrane / membrane / Glycoprotein 42
Function and homology information
Biological speciesMus musculus (house mouse)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. ...Bu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Immunity / Year: 2024
Title: Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells.
Authors: Bu, W. / Kumar, A. / Board, N.L. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I.
History
DepositionAug 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4C12 light chain
B: 4C12 heavy chain
C: 4C12 light chain
D: 4C12 heavy chain
E: 4C12 light chain
F: 4C12 light chain
G: 4C12 heavy chain
H: 4C12 heavy chain
I: Glycoprotein 42
J: Glycoprotein 42
K: Glycoprotein 42
L: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)258,81712
Polymers258,81712
Non-polymers00
Water3,441191
1
A: 4C12 light chain
B: 4C12 heavy chain
I: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 4C12 light chain
D: 4C12 heavy chain
J: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 4C12 light chain
H: 4C12 heavy chain
L: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: 4C12 light chain
G: 4C12 heavy chain
K: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.296, 63.568, 199.278
Angle α, β, γ (deg.)89.81, 89.75, 88.86
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
4C12 light chain


Mass: 23604.100 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
4C12 heavy chain


Mass: 25154.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein
Glycoprotein 42


Mass: 15946.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P03205
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM Tris pH7.5, 150mM NaCl, 0.2M zinc acetate dihydrate, and 18% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→66.42 Å / Num. obs: 73888 / % possible obs: 91.8 % / Redundancy: 3.8 % / Rsym value: 0.157 / Net I/σ(I): 5.4
Reflection shellResolution: 2.6→2.6 Å / Num. unique obs: 7047 / Rsym value: 1.187

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→53.51 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 3745 5.08 %
Rwork0.2256 --
obs0.2281 73652 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→53.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17022 0 0 191 17213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417488
X-RAY DIFFRACTIONf_angle_d0.81623901
X-RAY DIFFRACTIONf_dihedral_angle_d4.6172438
X-RAY DIFFRACTIONf_chiral_restr0.0512703
X-RAY DIFFRACTIONf_plane_restr0.0063047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.38061160.30652538X-RAY DIFFRACTION87
2.63-2.670.32751180.30132439X-RAY DIFFRACTION85
2.67-2.70.35211490.32256X-RAY DIFFRACTION83
2.7-2.740.43551040.28022239X-RAY DIFFRACTION78
2.74-2.780.33911480.27422584X-RAY DIFFRACTION91
2.78-2.830.33491400.2492673X-RAY DIFFRACTION95
2.83-2.870.32281250.25192687X-RAY DIFFRACTION95
2.87-2.920.31261370.25662708X-RAY DIFFRACTION95
2.92-2.980.34251370.25972701X-RAY DIFFRACTION95
2.98-3.030.34161400.262688X-RAY DIFFRACTION95
3.03-3.10.29641480.24362636X-RAY DIFFRACTION94
3.1-3.160.33511510.25362697X-RAY DIFFRACTION94
3.16-3.240.36931250.25482640X-RAY DIFFRACTION95
3.24-3.320.28551550.23662695X-RAY DIFFRACTION94
3.32-3.410.25231790.2242557X-RAY DIFFRACTION94
3.41-3.510.32961480.2212649X-RAY DIFFRACTION93
3.51-3.620.29551480.22862541X-RAY DIFFRACTION91
3.62-3.750.29981370.23272534X-RAY DIFFRACTION89
3.75-3.90.26471160.22292441X-RAY DIFFRACTION86
3.9-4.080.25761050.20012345X-RAY DIFFRACTION82
4.08-4.290.25491570.18472709X-RAY DIFFRACTION97
4.29-4.560.19581780.17632725X-RAY DIFFRACTION97
4.56-4.910.20521500.17142719X-RAY DIFFRACTION96
4.91-5.410.23641370.19252673X-RAY DIFFRACTION95
5.41-6.190.29161190.22382702X-RAY DIFFRACTION95
6.19-7.790.25131390.24732412X-RAY DIFFRACTION85
7.79-53.510.24171390.23722719X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 4.1318 Å / Origin y: -18.8885 Å / Origin z: 8.2062 Å
111213212223313233
T0.1289 Å20.0436 Å20.0162 Å2-0.5478 Å20.0904 Å2--0.3208 Å2
L-0.0109 °20.0094 °2-0.0379 °2-0.0387 °2-0.0162 °2--0.1162 °2
S0.0049 Å °-0.0113 Å °-0.0214 Å °0.0034 Å °0.0146 Å °-0.0025 Å °0.0024 Å °0.0152 Å °-0.0212 Å °
Refinement TLS groupSelection details: all

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