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- PDB-5sy8: Crystal structure of the complex of 10E8 Fab light chain mutant1 ... -

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Basic information

Entry
Database: PDB / ID: 5sy8
TitleCrystal structure of the complex of 10E8 Fab light chain mutant1 and T117v2 HIV-1 MPER scaffold
Components
  • 10E8 EPITOPE SCAFFOLD T117v2
  • 10E8 FAB HEAVY CHAIN
  • 10E8 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / HIV-1 GP41 MPER / 10E8 FAB / LIPID MEMBRANE
Function / homologyMannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsIrimia, A. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
Scripps CHAVI-IDUM1 AI100663 United States
CitationJournal: PLoS Pathog. / Year: 2017
Title: Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design.
Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / ...Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / Burton, D.R. / Schief, W.R. / Wilson, I.A.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 10E8 FAB HEAVY CHAIN
L: 10E8 FAB LIGHT CHAIN
O: 10E8 EPITOPE SCAFFOLD T117v2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2057
Polymers66,8373
Non-polymers3684
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-40 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.404, 56.596, 64.196
Angle α, β, γ (deg.)101.75, 101.19, 92.17
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody 10E8 FAB HEAVY CHAIN


Mass: 25318.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-15*05 / Plasmid: phCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human)
#2: Antibody 10E8 FAB LIGHT CHAIN


Mass: 22875.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-19*01 / Plasmid: phCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human)
#3: Protein 10E8 EPITOPE SCAFFOLD T117v2


Mass: 18643.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Star
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.21 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M Hepes pH 7.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.619→40.49 Å / Num. obs: 61518 / % possible obs: 86.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.943 / Rsym value: 0.087 / Net I/σ(I): 9.01
Reflection shellResolution: 1.619→1.65 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.753 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20002.3.8data reduction
HKL-20002.3.8data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6F, 3LF6

4g6f

3lf6


Resolution: 1.62→40.49 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.61
RfactorNum. reflection% reflection
Rfree0.214 3075 5 %
Rwork0.172 --
obs0.174 61470 86.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 24 351 4941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064904
X-RAY DIFFRACTIONf_angle_d1.0326708
X-RAY DIFFRACTIONf_dihedral_angle_d12.4781752
X-RAY DIFFRACTIONf_chiral_restr0.039738
X-RAY DIFFRACTIONf_plane_restr0.005883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6193-1.64470.3151220.25162305X-RAY DIFFRACTION76
1.6447-1.67160.28541370.23992603X-RAY DIFFRACTION85
1.6716-1.70040.29441400.23792667X-RAY DIFFRACTION87
1.7004-1.73140.29811420.21872683X-RAY DIFFRACTION86
1.7314-1.76470.26371350.20132575X-RAY DIFFRACTION85
1.7647-1.80070.24411340.1982530X-RAY DIFFRACTION83
1.8007-1.83980.23571330.18442526X-RAY DIFFRACTION83
1.8398-1.88260.22041470.17872791X-RAY DIFFRACTION90
1.8826-1.92970.24431410.17762699X-RAY DIFFRACTION89
1.9297-1.98190.24581450.17762745X-RAY DIFFRACTION89
1.9819-2.04020.21051430.1762706X-RAY DIFFRACTION88
2.0402-2.10610.23731380.17322642X-RAY DIFFRACTION87
2.1061-2.18130.23291310.17662490X-RAY DIFFRACTION80
2.1813-2.26870.21681430.18172713X-RAY DIFFRACTION89
2.2687-2.37190.28211470.17932791X-RAY DIFFRACTION91
2.3719-2.49690.26371440.18952731X-RAY DIFFRACTION90
2.4969-2.65330.20541440.19312740X-RAY DIFFRACTION89
2.6533-2.85820.21731320.1832502X-RAY DIFFRACTION82
2.8582-3.14570.22591500.18092856X-RAY DIFFRACTION93
3.1457-3.60060.19911450.15982757X-RAY DIFFRACTION90
3.6006-4.53540.17881360.13942563X-RAY DIFFRACTION84
4.5354-40.49770.16561460.15452780X-RAY DIFFRACTION91

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