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- PDB-5t85: Crystal structure of 10E8 Fab in complex with the MPER epitope sc... -

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Basic information

Entry
Database: PDB / ID: 5t85
TitleCrystal structure of 10E8 Fab in complex with the MPER epitope scaffold T117v2 and phosphatidylglycerol (06:0 PG)
Components
  • (Antibody 10E8 FAB ...) x 2
  • 10E8 EPITOPE SCAFFOLD T117V2
KeywordsIMMUNE SYSTEM / HIV-1 GP41 MPER / 10E8 FAB / LIPID MEMBRANE
Function / homology
Function and homology information


Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-44G / TRIETHYLENE GLYCOL
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.373 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
DepositionSep 6, 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 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody 10E8 FAB HEAVY CHAIN
L: Antibody 10E8 FAB LIGHT CHAIN
G: 10E8 EPITOPE SCAFFOLD T117V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8236
Polymers67,0803
Non-polymers7433
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-28 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.006, 67.287, 194.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailstrimer according to size exclusion chromatography

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Components

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Protein , 1 types, 1 molecules G

#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

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Antibody , 2 types, 2 molecules HL

#1: Antibody Antibody 10E8 FAB HEAVY CHAIN


Mass: 25447.475 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 Antibody 10E8 FAB LIGHT CHAIN


Mass: 22989.459 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)

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Non-polymers , 3 types, 149 molecules

#4: Chemical ChemComp-44G / (2S)-3-{[(R)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate


Mass: 442.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H35O10P
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: 50% PEG 200, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.373→48.669 Å / Num. obs: 28788 / % possible obs: 95.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 62 Å2 / CC1/2: 0.915 / Rsym value: 0.086 / Net I/σ(I): 8.5
Reflection shellResolution: 2.373→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.627 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-20002.3.7data reduction
HKL-20002.3.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6F, 3LF6
Resolution: 2.373→48.669 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.34
RfactorNum. reflection% reflection
Rfree0.2504 1437 5 %
Rwork0.1952 --
obs0.1979 28737 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2.373→48.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 33 146 4720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084715
X-RAY DIFFRACTIONf_angle_d1.1076423
X-RAY DIFFRACTIONf_dihedral_angle_d14.0321671
X-RAY DIFFRACTIONf_chiral_restr0.044713
X-RAY DIFFRACTIONf_plane_restr0.006832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3727-2.45760.31691390.28972636X-RAY DIFFRACTION94
2.4576-2.55590.34121450.26662769X-RAY DIFFRACTION98
2.5559-2.67230.32121450.25642748X-RAY DIFFRACTION98
2.6723-2.81310.30541410.24252681X-RAY DIFFRACTION95
2.8131-2.98940.25991440.23062742X-RAY DIFFRACTION97
2.9894-3.22010.3271470.23352778X-RAY DIFFRACTION97
3.2201-3.54410.28191410.21742708X-RAY DIFFRACTION96
3.5441-4.05670.24391400.1952653X-RAY DIFFRACTION93
4.0567-5.11020.20221470.14892793X-RAY DIFFRACTION95
5.1102-48.67970.22531480.17752792X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.2609-1.40853.24213.4802-1.41494.16690.2841-0.2249-0.25580.19850.11350.37250.7819-0.3291-0.34470.6041-0.03830.00680.5520.06080.55463.3399-8.497821.4542
23.0034-0.0835-0.06393.6323-1.28784.37860.0852-0.0970.01030.166-0.00330.5650.0016-0.0813-0.16650.64740.0058-0.09340.4719-0.0360.592821.8277-0.075249.2831
32.6452-0.28590.61414.0647-0.25293.3909-0.0624-0.11770.06950.56440.0793-0.1336-0.03250.080.0040.49120.0297-0.04020.5631-0.04510.4786.270910.618716.3882
42.2365-0.30810.13645.8024-0.3373.02310.0827-0.17030.0918-0.535-0.1144-0.4187-0.0120.13850.02530.65350.0313-0.05290.5158-0.01820.493132.678410.19442.9747
53.861-0.36520.55982.4918-1.05784.28790.19880.2924-0.5281-0.1103-0.1658-0.00480.21320.1732-0.02180.4395-0.0233-0.03180.4898-0.09830.606-23.8747-2.10610.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and ((resseq 1:113))
2X-RAY DIFFRACTION2chain 'H' and ((resseq 114:240))
3X-RAY DIFFRACTION3chain 'L' and ((resseq 1:106))
4X-RAY DIFFRACTION4chain 'L' and ((resseq 107:240))
5X-RAY DIFFRACTION5chain 'G' and ((resseq 11:162))

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