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- PDB-5t80: Crystal structure of 10E8 Fab in complex with the MPER epitope sc... -

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Basic information

Entry
Database: PDB / ID: 5t80
TitleCrystal structure of 10E8 Fab in complex with the MPER epitope scaffold T117v2 and phosphatidic acid (06:0 PA)
Components
  • 10E8 EPITOPE SCAFFOLD T117V2
  • Antibody 10E8 FAB HEAVY CHAIN
  • Antibody 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 / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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
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 1.2Dec 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 1.4Nov 13, 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: 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)67,4484
Polymers67,0803
Non-polymers3681
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-36 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.221, 67.262, 196.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 (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-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29O8P / Comment: phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.84 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 9.5 / Details: 50% PEG 400, 0.2M NaCl, 0.1 M CHES pH 9.5

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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: Apr 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.624→46.968 Å / Num. obs: 21918 / % possible obs: 97.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 75 Å2 / Rsym value: 0.075 / Net I/σ(I): 9.8
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.666 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20002.3.7data reduction
HKL-20002.3.7data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6F, 3LF6

4g6f

3lf6


Resolution: 2.62→46.97 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.95
RfactorNum. reflection% reflection
Rfree0.243 1091 5 %
Rwork0.184 --
obs0.187 21841 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.62→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4527 0 11 59 4597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094702
X-RAY DIFFRACTIONf_angle_d1.0876417
X-RAY DIFFRACTIONf_dihedral_angle_d14.3271673
X-RAY DIFFRACTIONf_chiral_restr0.043710
X-RAY DIFFRACTIONf_plane_restr0.006834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6237-2.74310.40361200.30642289X-RAY DIFFRACTION86
2.7431-2.88770.35151380.27122610X-RAY DIFFRACTION99
2.8877-3.06860.33781380.25942609X-RAY DIFFRACTION98
3.0686-3.30550.29041360.22542607X-RAY DIFFRACTION98
3.3055-3.6380.26731380.20782642X-RAY DIFFRACTION98
3.638-4.16420.28021380.17832608X-RAY DIFFRACTION96
4.1642-5.24530.19621390.14452662X-RAY DIFFRACTION98
5.2453-46.97550.20021440.16622723X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3759-0.0955-0.57095.149-0.45963.30390.2599-0.0780.14640.0706-0.1231-0.5885-0.10910.2264-0.17780.74860.04370.07210.6398-0.00250.835.82981.20349.8686
25.10691.9805-0.06584.48931.00913.71080.38160.01520.61860.1618-0.2093-0.0518-0.02760.1275-0.13240.6850.0632-0.02690.72740.03950.747250.84841.82360.5224
32.9785-1.488-2.72783.63650.34933.12820.0744-0.03970.31430.1240.246-0.1448-0.43180.1214-0.25330.6746-0.05110.04650.6595-0.10340.722624.02938.74921.6699
43.5055-1.0207-0.92974.47860.11573.3429-0.16660.1112-0.05870.32010.1916-0.02370.1099-0.3016-0.02080.70240.01580.04960.7323-0.00690.642620.3648-10.271616.3839
51.9017-0.6128-0.52775.01950.71523.15910.0041-0.07590.1263-0.61010.04690.2959-0.1366-0.0027-0.00090.8234-0.00560.09920.61990.0110.7225-5.3055-9.140143.9416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'H' AND ((RESSEQ 114:214))
2X-RAY DIFFRACTION2CHAIN 'G'
3X-RAY DIFFRACTION3CHAIN 'H' AND ((RESSEQ 1:113))
4X-RAY DIFFRACTION4CHAIN 'L' AND ((RESSEQ 1:107))
5X-RAY DIFFRACTION5CHAIN 'L' AND ((RESSEQ 108:220))

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