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

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Basic information

Entry
Database: PDB / ID: 9msp
TitleCrystal structure of MPXV A35R in complex with neutralizing antibody EV35-7
Components
  • EV35-7 heavy chain
  • EV35-7 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 / ACETATE ION / Protein OPG161
Function and homology information
Biological speciesMonkeypox virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsYuan, M. / 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
E: Protein OPG161
F: Protein OPG161
H: EV35-7 heavy chain
L: EV35-7 light chain
A: Protein OPG161
B: Protein OPG161
C: EV35-7 heavy chain
D: EV35-7 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,66814
Polymers140,1968
Non-polymers4716
Water8,233457
1
E: Protein OPG161
F: Protein OPG161
H: EV35-7 heavy chain
L: EV35-7 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3157
Polymers70,0984
Non-polymers2173
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein OPG161
B: Protein OPG161
C: EV35-7 heavy chain
D: EV35-7 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3527
Polymers70,0984
Non-polymers2543
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.339, 107.886, 268.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules EFAB

#1: 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

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Antibody , 2 types, 4 molecules HCLD

#2: Antibody EV35-7 heavy chain


Mass: 24098.092 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: Antibody EV35-7 light chain


Mass: 23171.699 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)

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Non-polymers , 4 types, 463 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% PEG 4000, 0.2 M ammonium sulfate, and 0.1 M acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 75918 / % possible obs: 98.7 % / Redundancy: 10 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.04 / Rrim(I) all: 0.125 / Χ2: 0.954 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.247.91.66336800.3080.6860.6161.7840.86998.9
2.24-2.287.81.4738090.3440.7160.5521.5790.8599.3
2.28-2.327.91.23537560.5220.8280.461.3250.91399.1
2.32-2.3781.03237610.6330.880.3851.1070.89398.5
2.37-2.428.10.88937310.7370.9210.330.9530.89297.3
2.42-2.487.50.70936820.7940.9410.2740.7640.94597.4
2.48-2.547.20.58436380.8050.9450.2330.6320.93795.2
2.54-2.618.90.50437800.9190.9790.1780.5360.96298.8
2.61-2.69100.37837940.9610.990.1250.3990.9899.7
2.69-2.7710.50.30938520.970.9920.0990.3241.01999.8
2.77-2.8710.90.23737990.9810.9950.0740.2491.04899.6
2.87-2.9911.30.18438090.9860.9970.0560.1921.06199.7
2.99-3.1211.60.13738420.990.9980.0410.1431.08399.5
3.12-3.2911.80.10338130.9940.9980.0310.1081.10599.4
3.29-3.4911.80.07638140.9960.9990.0230.081.0899.3
3.49-3.7611.70.06338320.9970.9990.0190.0661.06199.3
3.76-4.1411.40.0538780.9970.9990.0150.0530.95899.8
4.14-4.7410.40.04137300.9980.9990.0130.0430.88395.7
4.74-5.97120.03838300.9980.9990.0110.040.78698
5.97-5012.10.03340880.99910.010.0350.67299.7

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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: 2.19→44.74 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 3661 4.96 %
Rwork0.2109 --
obs0.2128 73826 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8916 0 27 457 9400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.626
X-RAY DIFFRACTIONf_dihedral_angle_d16.3823257
X-RAY DIFFRACTIONf_chiral_restr0.0451386
X-RAY DIFFRACTIONf_plane_restr0.0041579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.3239950.26311746X-RAY DIFFRACTION63
2.22-2.250.32661310.26812378X-RAY DIFFRACTION85
2.25-2.280.31951250.26672485X-RAY DIFFRACTION89
2.28-2.320.33171300.26712533X-RAY DIFFRACTION91
2.32-2.350.30671340.26052613X-RAY DIFFRACTION93
2.35-2.390.35331380.26362621X-RAY DIFFRACTION94
2.39-2.430.37421440.27252601X-RAY DIFFRACTION94
2.43-2.480.30391460.25722661X-RAY DIFFRACTION95
2.48-2.520.30031310.24942632X-RAY DIFFRACTION94
2.52-2.570.26241190.24892813X-RAY DIFFRACTION98
2.57-2.630.32931430.25132772X-RAY DIFFRACTION100
2.63-2.690.31671440.24562808X-RAY DIFFRACTION100
2.69-2.760.29861480.24212816X-RAY DIFFRACTION100
2.76-2.830.28091570.24722763X-RAY DIFFRACTION100
2.83-2.920.29951480.24972806X-RAY DIFFRACTION100
2.92-3.010.30781530.23992795X-RAY DIFFRACTION100
3.01-3.120.23721450.22452835X-RAY DIFFRACTION100
3.12-3.240.2911540.21562802X-RAY DIFFRACTION99
3.24-3.390.21111690.20722799X-RAY DIFFRACTION99
3.39-3.570.22011500.19972802X-RAY DIFFRACTION99
3.57-3.790.21781790.19172767X-RAY DIFFRACTION99
3.79-4.090.2311470.17842852X-RAY DIFFRACTION100
4.09-4.50.15831370.162841X-RAY DIFFRACTION99
4.5-5.150.1641170.15192699X-RAY DIFFRACTION93
5.15-6.480.22451350.18642908X-RAY DIFFRACTION100
6.48-44.740.23121420.19433017X-RAY DIFFRACTION99

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