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- PDB-5iq9: Crystal structure of 10E8v4 Fab in complex with an HIV-1 gp41 peptide. -

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Basic information

Entry
Database: PDB / ID: 5iq9
TitleCrystal structure of 10E8v4 Fab in complex with an HIV-1 gp41 peptide.
Components
  • 10E8v4 Heavy Chain
  • 10E8v4 Light Chain
  • gp41 MPER peptide
KeywordsIMMUNE SYSTEM / Immunoglobulin / MPER / Antibody
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation ...virus-mediated perturbation of host defense response => GO:0019049 / : / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / phagocytosis, engulfment / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of establishment of T cell polarity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / membrane => GO:0016020 / viral protein processing / blood microparticle / defense response to bacterium / fusion of virus membrane with host plasma membrane / external side of plasma membrane / innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Immunoglobulin lambda constant 2 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsOfek, G. / Kwon, Y.D. / Caruso, W. / Kwong, P.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: J.Virol. / Year: 2016
Title: Optimization of the Solubility of HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based Design.
Authors: Kwon, Y.D. / Georgiev, I.S. / Ofek, G. / Zhang, B. / Asokan, M. / Bailer, R.T. / Bao, A. / Caruso, W. / Chen, X. / Choe, M. / Druz, A. / Ko, S.Y. / Louder, M.K. / McKee, K. / O'Dell, S. / ...Authors: Kwon, Y.D. / Georgiev, I.S. / Ofek, G. / Zhang, B. / Asokan, M. / Bailer, R.T. / Bao, A. / Caruso, W. / Chen, X. / Choe, M. / Druz, A. / Ko, S.Y. / Louder, M.K. / McKee, K. / O'Dell, S. / Pegu, A. / Rudicell, R.S. / Shi, W. / Wang, K. / Yang, Y. / Alger, M. / Bender, M.F. / Carlton, K. / Cooper, J.W. / Blinn, J. / Eudailey, J. / Lloyd, K. / Parks, R. / Alam, S.M. / Haynes, B.F. / Padte, N.N. / Yu, J. / Ho, D.D. / Huang, J. / Connors, M. / Schwartz, R.M. / Mascola, J.R. / Kwong, P.D.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
A: 10E8v4 Heavy Chain
B: 10E8v4 Light Chain
H: 10E8v4 Heavy Chain
L: 10E8v4 Light Chain
C: gp41 MPER peptide
P: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)103,9626
Polymers103,9626
Non-polymers00
Water6,431357
1
A: 10E8v4 Heavy Chain
B: 10E8v4 Light Chain
C: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)51,9813
Polymers51,9813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-33 kcal/mol
Surface area21340 Å2
MethodPISA
2
H: 10E8v4 Heavy Chain
L: 10E8v4 Light Chain
P: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)51,9813
Polymers51,9813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-30 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.025, 79.529, 211.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 10E8v4 Heavy Chain


Mass: 25050.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment antigen-binding / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Gene: IGHG1 / Cell line (production host): Expi 293S / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Antibody 10E8v4 Light Chain


Mass: 22458.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment antigen-binding / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Gene: IGLC2 / Cell line (production host): Expi 293S / Production host: Homo sapiens (human) / References: UniProt: P0CG05
#3: Protein/peptide gp41 MPER peptide


Mass: 4471.073 Da / Num. of mol.: 2 / Fragment: UNP Residues 645-673 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q1HSF8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG3350, 25% Isopropanol, 0.1M Tris-HCl, 8.5, 10% Jeffamine.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 39438 / % possible obs: 87.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.073 / Rrim(I) all: 0.127 / Χ2: 0.84 / Net I/av σ(I): 9.312 / Net I/σ(I): 6.5 / Num. measured all: 101101
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.492.50.462191.1
2.49-2.592.50.364191.2
2.59-2.72.50.286190.3
2.7-2.852.50.217190.5
2.85-3.022.50.158189.3
3.02-3.262.50.126188.9
3.26-3.582.60.096187.9
3.58-4.12.60.091186.1
4.1-5.172.70.07183.4
5.17-502.80.058175.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
Cootmodel building
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6F

4g6f


Resolution: 2.4→36.448 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.92
RfactorNum. reflection% reflection
Rfree0.236 1895 4.96 %
Rwork0.1906 --
obs0.1928 38241 87.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.22 Å2 / Biso mean: 41.4955 Å2 / Biso min: 11.46 Å2
Refinement stepCycle: final / Resolution: 2.4→36.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 0 357 7343
Biso mean---42.77 -
Num. residues----910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037182
X-RAY DIFFRACTIONf_angle_d0.5359788
X-RAY DIFFRACTIONf_chiral_restr0.0421066
X-RAY DIFFRACTIONf_plane_restr0.0041246
X-RAY DIFFRACTIONf_dihedral_angle_d9.8424238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.31551350.26272671280691
2.46-2.52650.32841440.25562657280191
2.5265-2.60080.32971530.25142655280891
2.6008-2.68480.29381350.24012649278491
2.6848-2.78070.31651360.22712653278990
2.7807-2.8920.32641200.24052657277790
2.892-3.02350.29691510.22592625277689
3.0235-3.18280.25411300.21192614274488
3.1828-3.38210.25441410.1972609275089
3.3821-3.6430.20951380.18272610274887
3.643-4.00920.22131350.16662564269986
4.0092-4.58840.15081450.13842524266984
4.5884-5.77720.15791110.14332504261582
5.7772-36.45240.21921210.18072354247574
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)
12.20820.72410.70441.17770.28163.5280.0354-0.0436-0.07670.1072-0.0211-0.03180.03-0.1801-0.02840.2487-0.02690.03730.264-0.00110.2055-48.124132.8802-24.376
27.53692.1097-1.73112.8884-0.18914.642-0.01560.45820.03760.01080.0604-0.11370.0817-0.1059-0.03340.30060.0228-0.01380.27790.00210.1685-14.743847.163-10.7633
33.95742.18730.30544.4815-0.48543.8821-0.04540.1601-0.1187-0.1169-0.1391-0.0942-0.06440.15460.16040.1814-0.00950.02590.27910.00820.1488-36.371835.48-40.9874
42.5853-0.50131.94013.2355-2.968.2874-0.0550.3569-0.2673-0.12020.1401-0.01140.2535-0.292-0.1130.2233-0.04980.0270.4547-0.08530.2797-11.233135.0431-21.3318
53.9320.41-2.51941.2628-0.30374.18830.1235-0.10310.35010.1173-0.0157-0.0304-0.1247-0.0663-0.1270.2208-0.0151-0.03630.2199-0.02090.252-16.7315.9799-25.8127
68.12291.9751.97611.92240.80964.68730.04060.0609-0.18370.14640.07580.0965-0.0630.277-0.1270.27310.05130.02280.20560.00620.1809-50.1854-7.8008-11.8549
75.32242.40620.67253.16360.74132.87230.0420.26050.2592-0.2648-0.15560.0076-0.0255-0.13740.10240.23450.07240.00630.25690.03650.1802-28.57483.1045-42.374
83.3394-1.357-2.06643.6642.95489.0503-0.0458-0.02240.2074-0.04410.08450.0185-0.23610.2033-0.04780.162-0.0583-0.02920.2806-0.00450.2464-53.61624.0825-22.7959
95.36133.74871.78528.380.68811.7023-0.42630.870.2933-0.2257-0.71350.84590.4569-1.25991.12240.3789-0.17420.04230.7592-0.06480.4707-59.516220.8041-42.5362
103.04811.1468-1.50074.51084.72187.5023-0.00650.19070.6389-0.68-0.8307-1.2823-0.87020.85540.73080.4385-0.01370.17680.67950.29450.7308-5.316817.7227-44.0019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain H and resi 1:115H1 - 214
2X-RAY DIFFRACTION2chain H and resi 116:230H1 - 214
3X-RAY DIFFRACTION3chain L and resi 1:108L2 - 209
4X-RAY DIFFRACTION4chain L and resi 109:220L2 - 209
5X-RAY DIFFRACTION5chain A and resi 1:115A1 - 214
6X-RAY DIFFRACTION6chain A and resi 116:230A1 - 214
7X-RAY DIFFRACTION7chain B and resi 1:108B2 - 209
8X-RAY DIFFRACTION8chain B and resi 109:220B2 - 209
9X-RAY DIFFRACTION9chain PP667 - 684
10X-RAY DIFFRACTION10chain CC667 - 684

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