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- PDB-2y6s: Structure of an Ebolavirus-protective antibody in complex with it... -

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Basic information

Entry
Database: PDB / ID: 2y6s
TitleStructure of an Ebolavirus-protective antibody in complex with its mucin-domain linear epitope
Components
  • ENVELOPE GLYCOPROTEIN
  • HEAVY CHAIN
  • LIGHT CHAIN
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / lipid binding / host cell plasma membrane / virion membrane ...clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / lipid binding / host cell plasma membrane / virion membrane / extracellular region / membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
ZAIRE EBOLAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOlal, D.O. / Kuehne, A. / Lee, J.E. / Bale, S. / Dye, J.M. / Saphire, E.O.
CitationJournal: J.Virol. / Year: 2012
Title: Structure of an Ebola Virus-Protective Antibody in Complex with its Mucin-Domain Linear Epitope.
Authors: Olal, D.O. / Kuehne, A. / Bale, S. / Halfmann, P. / Hashiguchi, T. / Fusco, M.L. / Lee, J.E. / King, L.B. / Kawaoka, Y. / Dye, J.M. / Saphire, E.O.
History
DepositionJan 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 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
C: LIGHT CHAIN
D: HEAVY CHAIN
H: HEAVY CHAIN
L: LIGHT CHAIN
P: ENVELOPE GLYCOPROTEIN
Q: ENVELOPE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)96,3436
Polymers96,3436
Non-polymers00
Water86548
1
C: LIGHT CHAIN
D: HEAVY CHAIN
P: ENVELOPE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)48,1723
Polymers48,1723
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-32.4 kcal/mol
Surface area19590 Å2
MethodPISA
2
H: HEAVY CHAIN
L: LIGHT CHAIN
Q: ENVELOPE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)48,1723
Polymers48,1723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-32.7 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.554, 68.376, 92.827
Angle α, β, γ (deg.)90.00, 112.50, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN L AND (RESSEQ 1:217 )
211CHAIN C AND (RESSEQ 1:217 )
112CHAIN H AND (RESSEQ 1:126 OR RESSEQ 134:213 )
212CHAIN D AND (RESSEQ 1:126 OR RESSEQ 134:213 )
113CHAIN P AND (RESSEQ 478:492 )
213CHAIN Q AND (RESSEQ 478:492 )

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.420654, -0.009689, -0.90717), (-0.015606, -0.999872, 0.003443), (-0.907087, 0.012709, -0.420751)-0.09075, 4.55691, -0.13814
2given(0.42536, 0.000764, -0.905024), (-0.004493, -0.999986, -0.002956), (-0.905013, 0.005324, -0.42535)-0.33649, 4.28935, -0.14381
3given(0.447034, -0.012325, -0.894432), (-0.007423, -0.999922, 0.010069), (-0.894486, 0.002138, -0.447091)0.60088, 4.46003, -1.32527

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Components

#1: Antibody LIGHT CHAIN


Mass: 23762.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) MUS MUSCULUS (house mouse) / Organ: SPLEEN / Strain: BALB/C
#2: Antibody HEAVY CHAIN


Mass: 22797.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) MUS MUSCULUS (house mouse) / Organ: SPLEEN / Strain: BALB/C
#3: Protein/peptide ENVELOPE GLYCOPROTEIN / GP / GP1


Mass: 1611.946 Da / Num. of mol.: 2 / Fragment: RESIDUES 477-493 / Source method: obtained synthetically / Source: (synth.) ZAIRE EBOLAVIRUS / References: UniProt: P87666
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.62 Å3/Da / Density % sol: 53.1 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M BIS-TRIS PROPANE PH6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.82, 1.17
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: MIRRORS
RadiationMonochromator: SIDE SCATTERING BENT CUBE ROOT I BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.821
21.171
ReflectionResolution: 2.3→50 Å / Num. obs: 46342 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 44.75 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.9
Reflection shellResolution: 2.8→50 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.2 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DGG

3dgg


Resolution: 2.8→38.122 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 31.64 / Stereochemistry target values: ML / Details: RESIDUES 127-133 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2873 1235 5.1 %
Rwork0.2359 --
obs0.2386 24072 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.94 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.1396 Å20 Å2-6.1536 Å2
2---0.1047 Å20 Å2
3---7.2443 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 0 48 6704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036818
X-RAY DIFFRACTIONf_angle_d0.6769282
X-RAY DIFFRACTIONf_dihedral_angle_d12.2422418
X-RAY DIFFRACTIONf_chiral_restr0.0431070
X-RAY DIFFRACTIONf_plane_restr0.0041176
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1669X-RAY DIFFRACTIONPOSITIONAL
12C1669X-RAY DIFFRACTIONPOSITIONAL0.01
21H1559X-RAY DIFFRACTIONPOSITIONAL
22D1559X-RAY DIFFRACTIONPOSITIONAL0.01
31P100X-RAY DIFFRACTIONPOSITIONAL
32Q100X-RAY DIFFRACTIONPOSITIONAL0.008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.38481290.32772525X-RAY DIFFRACTION94
2.9121-3.04460.37821350.30142573X-RAY DIFFRACTION95
3.0446-3.2050.37561380.29412561X-RAY DIFFRACTION95
3.205-3.40570.3431530.27642565X-RAY DIFFRACTION95
3.4057-3.66850.3231430.25852534X-RAY DIFFRACTION95
3.6685-4.03730.32221510.2432572X-RAY DIFFRACTION94
4.0373-4.62060.23611320.19452577X-RAY DIFFRACTION94
4.6206-5.81810.19931360.18082562X-RAY DIFFRACTION93
5.8181-38.12520.22461180.20782368X-RAY DIFFRACTION84

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