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- PDB-9msn: Crystal structure of MPXV A35R in complex with neutralizing antib... -

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Basic information

Entry
Database: PDB / ID: 9msn
TitleCrystal structure of MPXV A35R in complex with neutralizing antibody EV35-2
Components
  • EV35-2 heavy chain
  • EV35-2 light chain
  • Protein OPG161
KeywordsIMMUNE SYSTEM / antibody / mpox / monkeypox / A35
Function / homologyChordopoxvirus A33R / Chordopoxvirus A33R protein / C-type lectin-like/link domain superfamily / host cell membrane / C-type lectin fold / virion membrane / membrane / Protein OPG161
Function and homology information
Biological speciesHomo sapiens (human)
Monkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsYuan, M. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142737 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI168631 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54CA267776 United States
CitationJournal: Cell / Year: 2025
Title: Human monoclonal antibodies targeting A35 protect from death caused by mpox.
Authors: Fantin, R.F. / Yuan, M. / Park, S.C. / Bozarth, B. / Cohn, H. / Ignacio, M. / Earl, P. / Civljak, A. / Laghlali, G. / Zhang, D. / Zhu, X. / Crandell, J. / Monteiro, V. / Clark, J.J. / ...Authors: Fantin, R.F. / Yuan, M. / Park, S.C. / Bozarth, B. / Cohn, H. / Ignacio, M. / Earl, P. / Civljak, A. / Laghlali, G. / Zhang, D. / Zhu, X. / Crandell, J. / Monteiro, V. / Clark, J.J. / Cotter, C. / Burkhardt, M. / Singh, G. / Warang, P. / Garcia-Bernalt Diego, J. / Srivastava, K. / Lugo, L.A. / Pischel, L. / Yildirim, I. / Omer, S.B. / da Silva, D. / Krammer, F. / Bajic, G. / Simon, V. / Schotsaert, M. / Lucas, C. / Wilson, I.A. / Moss, B. / Coelho, C.H.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EV35-2 heavy chain
B: EV35-2 light chain
J: Protein OPG161
K: Protein OPG161
H: EV35-2 heavy chain
L: EV35-2 light chain
E: Protein OPG161
F: Protein OPG161


Theoretical massNumber of molelcules
Total (without water)141,2068
Polymers141,2068
Non-polymers00
Water50428
1
A: EV35-2 heavy chain
B: EV35-2 light chain
E: Protein OPG161
F: Protein OPG161


Theoretical massNumber of molelcules
Total (without water)70,6034
Polymers70,6034
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: Protein OPG161
K: Protein OPG161
H: EV35-2 heavy chain
L: EV35-2 light chain


Theoretical massNumber of molelcules
Total (without water)70,6034
Polymers70,6034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.270, 130.226, 100.073
Angle α, β, γ (deg.)90.00, 116.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody EV35-2 heavy chain


Mass: 24253.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody EV35-2 light chain


Mass: 23521.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein
Protein OPG161


Mass: 11414.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG161, MPXVgp145 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A7H0DND2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 20% PEG 3350, 0.2 M K-formate, pH 7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9203 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9203 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 27452 / % possible obs: 97.7 % / Redundancy: 5.7 % / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.107 / Rrim(I) all: 0.264 / Χ2: 0.375 / Net I/σ(I): 2.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.95-34.10.81613590.3220.6980.4270.9270.17196
3-3.064.70.78113540.4820.8070.3810.8730.17798
3.06-3.1150.76514010.5840.8590.3640.8510.18499.2
3.11-3.185.30.71113720.6450.8860.3280.7850.19599.4
3.18-3.255.50.70814100.680.90.3220.780.20699.7
3.25-3.325.60.64813610.7620.930.2910.7120.21999.6
3.32-3.415.80.63914130.8170.9480.2820.70.24399.9
3.41-3.55.90.6214150.8270.9510.2710.6790.27799.9
3.5-3.65.80.89113880.8260.9510.3940.9780.29799.1
3.6-3.723.80.2859460.8630.9630.1420.321.66568.6
3.72-3.855.70.67613630.8930.9710.2980.7410.36396.1
3.85-460.42214050.9380.9840.1850.4620.39799.9
4-4.195.90.27813950.9610.990.1210.3040.388100
4.19-4.415.70.22813910.9680.9920.1020.2510.46599.8
4.41-4.685.40.19313970.9680.9920.0890.2130.51999.9
4.68-5.046.40.17214010.9810.9950.0730.1870.47499.9
5.04-5.556.50.1514100.9870.9970.0630.1630.39899.7
5.55-6.356.10.13914110.9850.9960.0610.1520.35799.8
6.35-87.20.10514310.9940.9990.0420.1130.37299.9
8-506.80.05114290.99810.0210.0550.65599.8

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→46.7 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3069 1367 5.04 %
Rwork0.28 --
obs0.2814 27099 94.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.92→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9281 0 0 28 9309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.788
X-RAY DIFFRACTIONf_dihedral_angle_d16.3583401
X-RAY DIFFRACTIONf_chiral_restr0.0481428
X-RAY DIFFRACTIONf_plane_restr0.0061659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.020.43311180.38322166X-RAY DIFFRACTION80
3.02-3.140.3611320.34352663X-RAY DIFFRACTION98
3.14-3.280.34681350.3232680X-RAY DIFFRACTION99
3.28-3.460.36121580.31432688X-RAY DIFFRACTION99
3.46-3.670.43191040.3942194X-RAY DIFFRACTION81
3.67-3.960.41481450.3452473X-RAY DIFFRACTION92
3.96-4.350.28571320.26012698X-RAY DIFFRACTION100
4.35-4.980.23811420.21552709X-RAY DIFFRACTION100
4.98-6.280.26921480.23092718X-RAY DIFFRACTION100
6.28-46.70.22431530.21762743X-RAY DIFFRACTION100

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