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- PDB-6cjk: Anti HIV Fab 10A -

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Basic information

Entry
Database: PDB / ID: 6cjk
TitleAnti HIV Fab 10A
Components
  • Immunoglobulin Fab heavy chain
  • Immunoglobulin Fab light chain
KeywordsIMMUNE SYSTEM / Fab / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.795 Å
AuthorsHangartner, L. / Ward, A.B. / Wilson, I.A. / Oyen, D.
Funding support United States, 2items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeIAVI SFP 2120/2121
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI100663 United States
CitationJournal: Immunity / Year: 2018
Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization.
Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton ...Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton / Andrew B Ward / Lars Hangartner /
Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 18, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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: Immunoglobulin Fab light chain
B: Immunoglobulin Fab heavy chain
C: Immunoglobulin Fab light chain
D: Immunoglobulin Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0968
Polymers92,8274
Non-polymers2694
Water9,854547
1
A: Immunoglobulin Fab light chain
B: Immunoglobulin Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5324
Polymers46,4142
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-28 kcal/mol
Surface area18220 Å2
MethodPISA
2
C: Immunoglobulin Fab light chain
D: Immunoglobulin Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5654
Polymers46,4142
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-31 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.173, 63.558, 72.649
Angle α, β, γ (deg.)67.99, 87.87, 76.73
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Immunoglobulin Fab light chain


Mass: 23047.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody Immunoglobulin Fab heavy chain


Mass: 23366.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 5.26, 0.17 M ammonium acetate, 15% glycerol, 19% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 1.795→40.703 Å / Num. obs: 73928 / % possible obs: 96.3 % / Redundancy: 3.2 % / CC1/2: 0.856 / Rpim(I) all: 0.048 / Rsym value: 0.074 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.795→40.703 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 3841 5.2 %
Rwork0.1633 --
obs0.1656 73915 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.795→40.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 18 547 6807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116616
X-RAY DIFFRACTIONf_angle_d1.0739106
X-RAY DIFFRACTIONf_dihedral_angle_d18.9412331
X-RAY DIFFRACTIONf_chiral_restr0.1691067
X-RAY DIFFRACTIONf_plane_restr0.0071169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.795-1.81770.3721070.36182155X-RAY DIFFRACTION78
1.8177-1.84160.39911130.33292405X-RAY DIFFRACTION90
1.8416-1.86680.32731180.30122516X-RAY DIFFRACTION92
1.8668-1.89350.2811100.27662619X-RAY DIFFRACTION94
1.8935-1.92180.32521560.26082537X-RAY DIFFRACTION95
1.9218-1.95180.28581540.23262564X-RAY DIFFRACTION95
1.9518-1.98380.28851360.21582621X-RAY DIFFRACTION96
1.9838-2.0180.21061270.20012583X-RAY DIFFRACTION95
2.018-2.05470.20031440.19422650X-RAY DIFFRACTION96
2.0547-2.09420.24851210.18542541X-RAY DIFFRACTION96
2.0942-2.1370.22961370.19382683X-RAY DIFFRACTION97
2.137-2.18340.23381360.1862599X-RAY DIFFRACTION96
2.1834-2.23420.21271210.17892634X-RAY DIFFRACTION97
2.2342-2.29010.23921270.17232583X-RAY DIFFRACTION96
2.2901-2.3520.20661490.16642635X-RAY DIFFRACTION97
2.352-2.42120.22871550.16992633X-RAY DIFFRACTION97
2.4212-2.49930.25811450.17262606X-RAY DIFFRACTION97
2.4993-2.58860.20441620.16552607X-RAY DIFFRACTION97
2.5886-2.69230.2071770.15662622X-RAY DIFFRACTION97
2.6923-2.81480.20841560.15022648X-RAY DIFFRACTION98
2.8148-2.96310.20381320.15212626X-RAY DIFFRACTION98
2.9631-3.14870.18121810.14372675X-RAY DIFFRACTION98
3.1487-3.39170.18051650.13772617X-RAY DIFFRACTION99
3.3917-3.73280.16871620.13512665X-RAY DIFFRACTION99
3.7328-4.27250.17761220.12612730X-RAY DIFFRACTION99
4.2725-5.38090.16781660.12252636X-RAY DIFFRACTION99
5.3809-40.71380.21041620.18622684X-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)
14.73464.1454-2.89615.3194-2.3332.99830.0545-0.35720.09130.255-0.06840.0369-0.0408-0.063-0.03860.25980.0311-0.07890.3489-0.0280.270417.75344.12416.9743
24.01810.2541.84471.5604-0.22563.7840.1158-0.2339-0.24970.1240.0185-0.10150.2022-0.2742-0.15920.17060.0109-0.00010.2763-0.00230.229819.6622-6.205814.3999
31.53190.6635-0.16792.2582-0.35980.9319-0.0573-0.01480.0542-0.1037-0.0015-0.137-0.01070.0510.06580.16460.00980.00690.224-0.00710.225922.2904-0.68256.7126
41.3394-0.9840.45252.57440.01660.6366-0.0233-0.07110.14220.18340.0483-0.087-0.024-0.0248-0.04020.15040.00260.06170.2434-0.01270.1978.45546.86628.137
55.7698-1.76240.45562.1573-0.29730.9758-0.3331-0.74370.52610.23160.2943-0.1138-0.0719-0.19040.080.24490.03480.00720.2905-0.08080.31441.583226.79998.2042
63.3093-1.62620.87911.6823-0.44191.1884-0.0372-0.3433-0.12990.24850.09090.2163-0.1417-0.2522-0.03140.24670.00630.04280.24570.00970.2926-1.263924.37758.4118
75.4998-4.73621.96614.2381-1.73740.7216-0.1946-0.22530.6860.21440.3741-0.4075-0.06930.0975-0.15710.37320.0717-0.00520.4146-0.16410.5237-2.393634.148510.5107
84.64582.5837-2.51144.63041.15984.9191-0.23080.67391.254-0.0140.5122-0.3172-0.37330.197-0.270.42790.03860.07370.3052-0.02670.499-1.909537.04986.0319
90.55960.23250.1041.1965-0.23960.5841-0.02320.0417-0.0047-0.02780.0858-0.02850.01280.0021-0.06680.1835-0.00410.01770.2312-0.01250.2006-0.2903-3.22720.973
102.10540.31712.61784.1990.64563.41420.0803-0.2985-0.11530.2516-0.2255-0.0587-0.05710.0950.15340.20950.015-0.01910.1266-0.04080.2719-1.135616.5172-0.125
114.56213.8486-1.48163.5449-1.82672.5744-0.13750.29440.242-0.21730.30210.2779-0.13780.0709-0.1120.21010.00820.02790.22230.01560.2734-3.667120.2217-10.002
124.1507-0.37893.12051.6393-0.56452.419-0.24440.79990.4188-0.49640.0018-0.1155-0.67230.64050.26540.5085-0.11720.01470.35450.06630.28454.83598.931335.8289
133.89430.26270.67452.3796-0.03174.4046-0.29640.04650.3349-0.23930.12530.1423-0.5973-0.21750.12710.2859-0.0167-0.0590.1935-0.01320.1914-5.90625.634837.4424
142.64020.49761.94210.72160.48483.2027-0.40660.07280.4727-0.10820.05210.2168-0.8592-0.0350.31520.38880.0193-0.05650.1932-0.01240.2514-5.19179.904638.9529
151.7877-1.2480.41382.2049-0.15960.76130.04510.171-0.1577-0.0197-0.022-0.09690.24120.226-0.00350.29720.00790.0210.2719-0.03220.232813.9664-15.479843.9713
163.7093-2.8561-4.58997.9336.24666.94020.1911.1706-0.6113-0.64980.0131-0.28980.31310.1037-0.10570.4890.1185-0.06840.5741-0.21880.412817.9614-29.946537.4901
172.84190.56250.71033.83464.72925.869-0.19170.5157-0.1898-0.13630.284-0.57180.20430.5202-0.10760.26860.04340.05290.3860.01670.393125.428-23.181544.915
185.3183.12891.93543.69734.25875.97990.38580.2283-0.86570.7062-0.2757-0.45621.11010.366-0.00440.40920.0961-0.00640.27370.01770.452523.9426-28.621449.0454
191.7689-0.36450.46571.7469-0.00242.3009-0.1141-0.3528-0.1120.14510.06980.29730.0152-0.46810.07660.2201-0.00740.00210.34780.03890.1982-17.6087-8.395431.3476
202.42980.90392.35731.6966-0.62013.87830.03530.04150.0342-0.035-0.05050.0333-0.2603-0.15950.010.24410.0165-0.00650.2478-0.0050.2081-14.8734-0.17826.7303
211.6034-0.21940.61620.64660.27251.2265-0.0099-0.13970.05970.1085-0.0180.0682-0.0308-0.25630.02620.24430.00970.00740.330.00990.2136-14.916-5.748427.9013
223.1453-2.16770.44535.6341-5.06245.54990.39930.0842-0.4531-0.4353-0.24870.20381.1005-0.3008-0.1610.397-0.0618-0.08150.2713-0.00340.2691-4.8759-23.458828.1134
233.5238-1.0867-1.91645.56121.59633.77190.1167-0.5409-0.23750.1930.2544-0.29171.00991.1413-0.43360.38560.1136-0.04720.405-0.01360.276112.7937-32.143152.5691
241.7059-0.6430.55931.9934-0.43176.13080.0469-0.1082-0.0547-0.02440.04820.18630.67670.0073-0.09680.3455-0.0759-0.02220.2340.0220.2590.6175-24.934144.4073
253.37061.67470.63773.4949-0.98220.743-0.08860.09230.2606-0.25920.09990.1330.24230.17240.09750.2929-0.0094-0.0480.2265-0.01570.29793.8404-20.371741.5924
261.97150.3842.21290.75750.05725.8771-0.0157-0.18010.0417-0.2382-0.07990.12660.2233-0.30150.10080.3264-0.0021-0.04040.2465-0.00790.27971.1921-26.729349.3364
271.8271-2.39541.46923.6696-2.18861.9548-0.4136-0.024-0.25890.16220.19340.17-0.02550.03920.17620.5614-0.1067-0.08420.29610.04660.4047-1.9668-32.660947.2047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:17 )A2 - 17
2X-RAY DIFFRACTION2( CHAIN A AND RESID 18:38 )A18 - 38
3X-RAY DIFFRACTION3( CHAIN A AND RESID 39:83 )A39 - 83
4X-RAY DIFFRACTION4( CHAIN A AND RESID 84:128 )A84 - 128
5X-RAY DIFFRACTION5( CHAIN A AND RESID 129:149 )A129 - 149
6X-RAY DIFFRACTION6( CHAIN A AND RESID 150:187 )A150 - 187
7X-RAY DIFFRACTION7( CHAIN A AND RESID 188:197 )A188 - 197
8X-RAY DIFFRACTION8( CHAIN A AND RESID 198:211 )A198 - 211
9X-RAY DIFFRACTION9( CHAIN B AND RESID 4:157 )B4 - 157
10X-RAY DIFFRACTION10( CHAIN B AND RESID 158:175 )B158 - 175
11X-RAY DIFFRACTION11( CHAIN B AND RESID 176:211 )B176 - 211
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1:25 )C1 - 25
13X-RAY DIFFRACTION13( CHAIN C AND RESID 26:48 )C26 - 48
14X-RAY DIFFRACTION14( CHAIN C AND RESID 49:95 )C49 - 95
15X-RAY DIFFRACTION15( CHAIN C AND RESID 96:173 )C96 - 173
16X-RAY DIFFRACTION16( CHAIN C AND RESID 174:186 )C174 - 186
17X-RAY DIFFRACTION17( CHAIN C AND RESID 187:199 )C187 - 199
18X-RAY DIFFRACTION18( CHAIN C AND RESID 200:211 )C200 - 211
19X-RAY DIFFRACTION19( CHAIN D AND RESID 4:39 )D4 - 39
20X-RAY DIFFRACTION20( CHAIN D AND RESID 40:59 )D40 - 59
21X-RAY DIFFRACTION21( CHAIN D AND RESID 60:106 )D60 - 106
22X-RAY DIFFRACTION22( CHAIN D AND RESID 107:119 )D107 - 119
23X-RAY DIFFRACTION23( CHAIN D AND RESID 120:134 )D120 - 134
24X-RAY DIFFRACTION24( CHAIN D AND RESID 135:157 )D135 - 157
25X-RAY DIFFRACTION25( CHAIN D AND RESID 158:175 )D158 - 175
26X-RAY DIFFRACTION26( CHAIN D AND RESID 176:200 )D176 - 200
27X-RAY DIFFRACTION27( CHAIN D AND RESID 201:210 )D201 - 210

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