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- PDB-12qa: Crystal structure of CM10 Fab in complex with an orthomarburgviru... -

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Basic information

Entry
Database: PDB / ID: 12qa
TitleCrystal structure of CM10 Fab in complex with an orthomarburgvirus GP2 peptide
Components
  • CM10 Fab heavy chain
  • CM10 Fab light chain
  • GP2 peptide
KeywordsIMMUNE SYSTEM / orthomarburgvirus / cross-reactive / antibody / GP2
Function / homology
Function and homology information


fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
TLV/ENV coat polyprotein / Filoviruses glycoprotein / : / Filoviruses glycoprotein, extracellular domain / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Orthomarburgvirus marburgense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNiyongabo, A. / Janus, B.M. / Metcalf, M. / Ofek, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Crystal structure of CM10 Fab in complex with an orthomarburgvirus GP2 peptide
Authors: Niyongabo, A. / Janus, B.M. / Metcalf, M. / Ofek, G.
History
DepositionApr 14, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CM10 Fab light chain
H: CM10 Fab heavy chain
P: GP2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4155
Polymers49,3353
Non-polymers802
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-54 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.222, 41.687, 80.643
Angle α, β, γ (deg.)90.00, 102.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody CM10 Fab light chain


Mass: 24045.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Macaca mulatta (Rhesus monkey)
#2: Antibody CM10 Fab heavy chain


Mass: 23630.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Macaca mulatta (Rhesus monkey)
#3: Protein/peptide GP2 peptide


Mass: 1658.804 Da / Num. of mol.: 1 / Fragment: residues 450-464 / Source method: obtained synthetically / Source: (synth.) Orthomarburgvirus marburgense / References: UniProt: Q1PDC7
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 3% DMSO, 30%(v/v) MPD, 15%(w/v) PEG 8000, 0.1M Calcium Chloride, 0.1M Sodium Acetate/Acetic Acid pH 4.5

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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 EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 50772 / % possible obs: 87.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.4
Reflection shellResolution: 1.6→1.658 Å / Rmerge(I) obs: 0.618 / Num. unique obs: 3822

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.85 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1879 3.7 %
Rwork0.1754 --
obs0.1766 50757 87.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 2 393 3812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018
X-RAY DIFFRACTIONf_angle_d1.391
X-RAY DIFFRACTIONf_dihedral_angle_d13.2161277
X-RAY DIFFRACTIONf_chiral_restr0.092542
X-RAY DIFFRACTIONf_plane_restr0.009622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.36681030.28172739X-RAY DIFFRACTION64
1.64-1.690.35011250.26023211X-RAY DIFFRACTION76
1.69-1.750.27521320.23433461X-RAY DIFFRACTION81
1.75-1.810.26381400.21943607X-RAY DIFFRACTION84
1.81-1.880.20681410.21233738X-RAY DIFFRACTION87
1.88-1.970.22221460.19413796X-RAY DIFFRACTION89
1.97-2.070.23481480.17613788X-RAY DIFFRACTION89
2.07-2.20.20631470.164028X-RAY DIFFRACTION94
2.2-2.370.20741600.16184059X-RAY DIFFRACTION95
2.37-2.610.19411590.15944105X-RAY DIFFRACTION95
2.61-2.990.21071540.16283979X-RAY DIFFRACTION93
2.99-3.760.18851620.15614186X-RAY DIFFRACTION96
3.76-36.850.17831620.17334181X-RAY DIFFRACTION94

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