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- PDB-5tfw: Crystal structure of 10E8 Fab light chain mutant2 against the MPE... -

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Basic information

Entry
Database: PDB / ID: 5tfw
TitleCrystal structure of 10E8 Fab light chain mutant2 against the MPER region of the HIV-1 Env, in complex with T117v2 epitope scaffold
Components
  • (Antibody 10E8 FAB ...) x 2
  • 10E8 EPITOPE SCAFFOLD T117V2
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 / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.168 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 26, 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 6, 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
H: Antibody 10E8 FAB HEAVY CHAIN
L: Antibody 10E8 FAB LIGHT CHAIN MUTANT2
O: 10E8 EPITOPE SCAFFOLD T117V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1225
Polymers66,9543
Non-polymers1682
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-30 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.490, 63.410, 53.870
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules O

#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 MUTANT2


Mass: 22863.111 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, 233 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 6.9
Details: 0.2 M Na thiocyanate, 20% PEG 3350, pH 6.9, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.168→47.235 Å / Num. obs: 36138 / % possible obs: 94.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 41 Å2 / CC1/2: 0.999 / Rsym value: 0.056 / Net I/σ(I): 15.5
Reflection shellResolution: 2.168→2.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.835 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSVERSION November 3, 2014data reduction
XSCALEVERSION November 3, 2014 BUILT=20141118data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6F, 3LF6

4g6f

3lf6


Resolution: 2.168→47.235 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1805 5 %
Rwork0.1693 --
obs0.1721 36126 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59 Å2
Refinement stepCycle: LAST / Resolution: 2.168→47.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 11 231 4787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074739
X-RAY DIFFRACTIONf_angle_d0.8716476
X-RAY DIFFRACTIONf_dihedral_angle_d13.7542803
X-RAY DIFFRACTIONf_chiral_restr0.055719
X-RAY DIFFRACTIONf_plane_restr0.005843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1683-2.22690.32871410.29462671X-RAY DIFFRACTION96
2.2269-2.29240.3296820.26631564X-RAY DIFFRACTION57
2.2924-2.36640.27151470.23792804X-RAY DIFFRACTION100
2.3664-2.4510.28321460.21622780X-RAY DIFFRACTION100
2.451-2.54910.27321450.20282757X-RAY DIFFRACTION100
2.5491-2.66520.25121450.19592767X-RAY DIFFRACTION100
2.6652-2.80560.24841460.19082761X-RAY DIFFRACTION100
2.8056-2.98140.27581470.19082814X-RAY DIFFRACTION100
2.9814-3.21160.24571470.18692786X-RAY DIFFRACTION100
3.2116-3.53460.28281350.18072558X-RAY DIFFRACTION92
3.5346-4.04590.21891240.15642366X-RAY DIFFRACTION84
4.0459-5.09640.17451480.12662817X-RAY DIFFRACTION100
5.0964-47.24630.18021520.13922876X-RAY DIFFRACTION99
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)
12.90380.5956-0.50772.081-0.65573.5732-0.16990.2369-0.1357-0.2339-0.1214-0.06450.00290.07820.26630.35820.05820.01250.3877-0.01680.24-46.29926.7823-9.1399
22.72760.42111.20832.06930.37071.83760.28250.0765-0.6472-0.24120.2268-0.20710.12280.0993-0.46270.35430.0356-0.07090.82270.02360.5706-12.425524.2786-18.5515
33.10930.2449-0.11951.72420.36032.2776-0.0005-0.0556-0.08590.1511-0.1377-0.15440.04590.29430.12880.3190.0151-0.02270.43260.07880.2488-40.358828.83829.7308
42.6826-0.6470.72812.25690.98162.79210.12980.08750.0273-0.30340.162-0.0354-0.5029-0.0755-0.3190.37770.02780.09310.75470.0820.6094-6.868636.1333-9.3199
53.5898-0.0442-0.90622.99890.61431.8280.15490.13490.29810.3491-0.39571.0225-0.078-0.6060.19710.46990.00420.10910.6848-0.15620.7198-74.381627.937812.707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and ((resseq 1:108))
2X-RAY DIFFRACTION2chain 'L' and ((resseq 109:214))
3X-RAY DIFFRACTION3chain 'H' and ((resseq 1:130))
4X-RAY DIFFRACTION4chain 'H' and ((resseq 131:234))
5X-RAY DIFFRACTION5chain 'O'

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