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- PDB-5iq7: Crystal structure of 10E8-S74W Fab in complex with an HIV-1 gp41 ... -

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Basic information

Entry
Database: PDB / ID: 5iq7
TitleCrystal structure of 10E8-S74W Fab in complex with an HIV-1 gp41 peptide.
Components
  • 10E8-S74W Heavy Chain
  • 10E8-S74W Light Chain
  • gp41 MPER peptide
KeywordsIMMUNE SYSTEM / Immunoglobulin / MPER / Antibody
Function / homology
Function and homology information


: / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Fc epsilon receptor (FCERI) signaling ...: / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / phagocytosis, engulfment / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / antigen binding / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / clathrin-dependent endocytosis of virus by host cell / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / viral protein processing / 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 / virion membrane / structural molecule activity / 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: 3.2869 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 1.1Apr 27, 2016Group: Source and taxonomy
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 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 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 10E8-S74W Heavy Chain
L: 10E8-S74W Light Chain
P: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)52,5123
Polymers52,5123
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-32 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.762, 189.257, 71.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody 10E8-S74W Heavy Chain


Mass: 25171.182 Da / Num. of mol.: 1 / Mutation: S74W,S74W
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 10E8-S74W Light Chain


Mass: 22712.158 Da / Num. of mol.: 1
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: 4628.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: V9QIE5

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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: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 40% PEG400, 0.1M NaCitrate, 0.1M Tris-HCl, 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 14165 / % possible obs: 98.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 114.84 Å2 / Rmerge(I) obs: 0.111 / Net I/av σ(I): 19.672 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.27-3.344.80.627185.1
3.34-3.415.50.545192.9
3.41-3.496.40.578198.5
3.49-3.587.50.481199.6
3.58-3.678.60.4611100
3.67-3.789.60.4511100
3.78-3.910.10.3581100
3.9-4.0410.20.2751100
4.04-4.210.10.211100
4.2-4.39100.1561100
4.39-4.639.90.1361100
4.63-4.929.80.1241100
4.92-5.39.80.1071100
5.3-5.83100.0991100
5.83-6.679.80.0851100
6.67-8.49.20.0631100
8.4-507.10.046198.6

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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: 3.2869→37.512 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.44
RfactorNum. reflection% reflection
Rfree0.282 711 5.03 %
Rwork0.2303 --
obs0.2328 14140 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 294.53 Å2 / Biso mean: 145.5905 Å2 / Biso min: 26.12 Å2
Refinement stepCycle: final / Resolution: 3.2869→37.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 0 0 3640
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053744
X-RAY DIFFRACTIONf_angle_d0.6855104
X-RAY DIFFRACTIONf_chiral_restr0.043552
X-RAY DIFFRACTIONf_plane_restr0.005651
X-RAY DIFFRACTIONf_dihedral_angle_d10.792198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2869-3.54060.38831340.33042409254389
3.5406-3.89650.36571460.28862692283899
3.8965-4.45960.26561510.228827022853100
4.4596-5.61560.21511260.214827662892100
5.6156-37.51470.29081540.210928603014100
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)
15.5725-2.78870.60676.37733.68728.82210.5868-0.5184-1.02390.5696-0.32030.5465-0.1716-2.1243-0.35961.2091-0.05030.21391.21420.18621.320550.171512.814893.3882
26.10432.25295.19946.9986-3.25669.0912-0.3694-0.10020.1537-0.02590.43-0.3779-0.7297-0.6034-0.0521.0013-0.04450.03470.9129-0.07850.753755.30813.992783.1037
37.074-5.6778-2.97994.57632.5672.33362.2931-1.0482-0.6167-0.9784-1.4199-0.2203-0.8584-2.8893-1.67831.03120.0227-0.02891.3616-0.29341.182168.24116.838283.36
40.3897-0.12550.0264.0496-2.53231.80640.807-0.07031.276-0.0827-0.4824-1.5362-1.55810.86240.19481.6859-0.248-0.05271.304-0.03831.195763.297722.479487.4591
59.02634.23720.69832.168-0.7947.72940.1322-1.0677-0.61040.5446-0.4561-0.33661.5848-0.60.70281.24360.0595-0.06651.15210.05991.203659.12098.857992.6831
63.285-3.4174-1.88867.03550.79736.20440.0867-0.12170.4769-0.84520.5835-1.3027-0.74480.5140.07670.72850.0173-0.00651.03010.03330.81354.005719.165286.5115
76.66016.43847.57759.47469.47762.0091-0.29164.09470.9198-4.23512.1226-2.6069-5.16772.9594-1.72531.83640.23170.15141.2362-0.06210.933467.224412.546563.407
87.2646-3.1063-3.4575.83663.84479.7023-0.9988-0.7311-1.4049-0.121-0.3031-0.57741.36791.61931.32321.16270.10850.09371.0630.02081.238154.516911.041675.2815
95.52330.3787-2.77874.6103-5.87088.85290.67520.0254-0.54270.9844-0.46030.36-0.0464-2.54130.18840.88890.253-0.15391.5427-0.04251.346545.264819.186191.8837
103.3758-0.13173.88093.6289-3.47347.47430.44-1.1912-0.20761.1140.9051-0.9151-1.8443-1.3064-0.89031.29230.6965-0.01011.839-0.09171.144437.262243.537197.442
114.36741.4427-4.0925.71051.54655.4567-3.62393.49010.5195-5.06123.8141-0.64560.7931-4.28880.2092.6139-0.4563-0.0132.73670.3341.797830.030457.371576.6523
123.0442-1.81474.19817.5579-0.41696.9980.37170.16970.1967-1.0531-0.3710.28921.1472-1.7024-0.27351.8830.51440.05792.19550.03371.000229.480843.233291.385
135.0496-3.98466.70557.8352-6.66839.2717-0.35411.412-1.9266-0.56810.63380.31770.40440.42550.18221.73070.3520.22571.8297-0.12511.082932.480139.449588.0174
144.51260.4452-0.74814.128-4.69175.41161.51561.96851.3635-2.74-1.70020.40620.9812-0.66830.05911.42840.6896-0.22252.52770.1551.096724.192351.122682.2853
156.9778-1.3693-0.23860.98770.57822.73420.29070.252-0.39370.59960.56571.5994-0.9696-1.5663-0.66861.50930.55560.0541.8079-0.06141.073625.564649.065894.6561
168.6636-2.2798-2.05958.6278-4.81466.11830.20641.5729-0.3744-0.8954-0.22780.08280.5311-0.81740.02641.12570.0959-0.05770.9726-0.15780.667748.29721.685667.8656
177.8995-0.95840.26363.0488-2.8293.2992-0.21171.5435-0.2423-0.85580.2090.09180.158-0.1466-0.02481.5632-0.041-0.05861.7533-0.2521.098348.008416.586465.323
183.8368-0.67610.31090.6916-1.21090.54820.0851-0.1598-0.9721-0.0680.43040.34480.3583-0.7619-0.27091.17890.082-0.21511.7738-0.18231.159942.004530.432871.7695
192.7562.88820.43428.25981.0755.19180.6466-0.0875-0.02860.617-0.20510.0903-0.2976-0.4005-0.44371.27850.37330.00141.70680.05630.878341.339545.982978.9908
208.60894.20518.88998.90012.66039.49611.57831.2145-1.56910.1087-0.4124-0.22212.31811.6003-1.36691.5925-0.03790.26181.3045-0.05051.564584.29031.664278.0865
215.414-1.70962.37842.6723-4.24076.73470.3815-0.6536-0.95030.9588-1.24891.0464-2.84610.14561.69251.85680.39020.21930.8703-0.0321.3173.687910.491167.5572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 25 )H1 - 25
2X-RAY DIFFRACTION2chain 'H' and (resid 26 through 51 )H26 - 51
3X-RAY DIFFRACTION3chain 'H' and (resid 52 through 56 )H52 - 56
4X-RAY DIFFRACTION4chain 'H' and (resid 57 through 66 )H57 - 66
5X-RAY DIFFRACTION5chain 'H' and (resid 67 through 82 )H67 - 82
6X-RAY DIFFRACTION6chain 'H' and (resid 82A through 98 )H82 - 98
7X-RAY DIFFRACTION7chain 'H' and (resid 99 through 100H)H99 - 100
8X-RAY DIFFRACTION8chain 'H' and (resid 100I through 103 )H100 - 103
9X-RAY DIFFRACTION9chain 'H' and (resid 104 through 112 )H104 - 112
10X-RAY DIFFRACTION10chain 'H' and (resid 113 through 124 )H113 - 124
11X-RAY DIFFRACTION11chain 'H' and (resid 125 through 134 )H125 - 134
12X-RAY DIFFRACTION12chain 'H' and (resid 135 through 157 )H135 - 157
13X-RAY DIFFRACTION13chain 'H' and (resid 158 through 177 )H158 - 177
14X-RAY DIFFRACTION14chain 'H' and (resid 178 through 189 )H178 - 189
15X-RAY DIFFRACTION15chain 'H' and (resid 190 through 214 )H190 - 214
16X-RAY DIFFRACTION16chain 'L' and (resid 2 through 48 )L2 - 48
17X-RAY DIFFRACTION17chain 'L' and (resid 49 through 94 )L49 - 94
18X-RAY DIFFRACTION18chain 'L' and (resid 95 through 119 )L95 - 119
19X-RAY DIFFRACTION19chain 'L' and (resid 120 through 211 )L120 - 211
20X-RAY DIFFRACTION20chain 'P' and (resid 656 through 670 )P656 - 670
21X-RAY DIFFRACTION21chain 'P' and (resid 671 through 685 )P671 - 685

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