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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
Specimen sourceOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.795 Å resolution
AuthorsHangartner, L. / Ward, A.B. / Wilson, I.A. / Oyen, D.
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 / 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 26, 2018 / Release: Aug 15, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 15, 2018Structure modelrepositoryInitial release
1.1Aug 29, 2018Structure modelData collection / Database referencescitation_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
Polyers92,8274
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
Polyers46,4142
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3510
ΔGint (kcal/M)-28
Surface area (Å2)18220
MethodPISA
2
C: Immunoglobulin Fab light chain
D: Immunoglobulin Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5654
Polyers46,4142
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3600
ΔGint (kcal/M)-31
Surface area (Å2)18530
MethodPISA
Unit cell
γ
α
β
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-MP 1

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Components

#1: Protein/peptide Immunoglobulin Fab light chain


Mass: 23047.424 Da / Num. of mol.: 2 / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Protein/peptide Immunoglobulin Fab heavy chain


Mass: 23366.195 Da / Num. of mol.: 2 / 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 / Formula: C2H3O2 / Acetate
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3 / Glycerol
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Formula: H2O / Water

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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 / Density percent sol: 46.37 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 23-ID-D / Synchrotron site: APS / Beamline: 23-ID-D / Wavelength: 1.03315
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: Oct 15, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionD resolution high: 1.795 Å / D resolution low: 40.703 Å / Number obs: 73928 / CC half: 0.856 / Rpim I all: 0.048 / Rsym value: 0.074 / NetI over sigmaI: 16.5 / Redundancy: 3.2 % / Percent possible obs: 96.3
Reflection shellHighest resolution: 1.8 Å / Lowest resolution: 1.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefineOverall SU ML: 0.25 / Cross valid method: FREE R-VALUE / Sigma F: 1.96 / Overall phase error: 23.3 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2056 / R factor R work: 0.1633 / R factor obs: 0.1656 / Highest resolution: 1.795 Å / Lowest resolution: 40.703 Å / Number reflection R free: 3841 / Number reflection obs: 73915 / Percent reflection R free: 5.2 / Percent reflection obs: 95.87
Refine hist #LASTHighest resolution: 1.795 Å / Lowest resolution: 40.703 Å
Number of atoms included #LASTProtein: 6242 / Nucleic acid: 0 / Ligand: 18 / Solvent: 547 / Total: 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
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.79500.37200.36181.8177107215578.00
1.81770.39910.33291.8416113240590.00
1.84160.32730.30121.8668118251692.00
1.86680.28100.27661.8935110261994.00
1.89350.32520.26081.9218156253795.00
1.92180.28580.23261.9518154256495.00
1.95180.28850.21581.9838136262196.00
1.98380.21060.20012.0180127258395.00
2.01800.20030.19422.0547144265096.00
2.05470.24850.18542.0942121254196.00
2.09420.22960.19382.1370137268397.00
2.13700.23380.18602.1834136259996.00
2.18340.21270.17892.2342121263497.00
2.23420.23920.17232.2901127258396.00
2.29010.20660.16642.3520149263597.00
2.35200.22870.16992.4212155263397.00
2.42120.25810.17262.4993145260697.00
2.49930.20440.16552.5886162260797.00
2.58860.20700.15662.6923177262297.00
2.69230.20840.15022.8148156264898.00
2.81480.20380.15212.9631132262698.00
2.96310.18120.14373.1487181267598.00
3.14870.18050.13773.3917165261799.00
3.39170.16870.13513.7328162266599.00
3.73280.17760.12614.2725122273099.00
4.27250.16780.12255.3809166263699.00
5.38090.21040.186240.7138162268499.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
14.73464.1454-2.89615.3194-2.33302.99830.0545-0.35720.09130.2550-0.06840.0369-0.0408-0.0630-0.03860.25980.0311-0.07890.3489-0.02800.270417.75344.124016.9743
24.01810.25401.84471.5604-0.22563.78400.1158-0.2339-0.24970.12400.0185-0.10150.2022-0.2742-0.15920.17060.0109-0.00010.2763-0.00230.229819.6622-6.205814.3999
31.53190.6635-0.16792.2582-0.35980.9319-0.0573-0.01480.0542-0.1037-0.0015-0.1370-0.01070.05100.06580.16460.00980.00690.2240-0.00710.225922.2904-0.68256.7126
41.3394-0.98400.45252.57440.01660.6366-0.0233-0.07110.14220.18340.0483-0.0870-0.0240-0.0248-0.04020.15040.00260.06170.2434-0.01270.19708.45546.86628.1370
55.7698-1.76240.45562.1573-0.29730.9758-0.3331-0.74370.52610.23160.2943-0.1138-0.0719-0.19040.08000.24490.03480.00720.2905-0.08080.31441.583226.79998.2042
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
75.4998-4.73621.96614.2381-1.73740.7216-0.1946-0.22530.68600.21440.3741-0.4075-0.06930.0975-0.15710.37320.0717-0.00520.4146-0.16410.5237-2.393634.148510.5107
84.64582.5837-2.51144.63041.15984.9191-0.23080.67391.2540-0.01400.5122-0.3172-0.37330.1970-0.27000.42790.03860.07370.3052-0.02670.4990-1.909537.04986.0319
90.55960.23250.10401.1965-0.23960.5841-0.02320.0417-0.0047-0.02780.0858-0.02850.01280.0021-0.06680.1835-0.00410.01770.2312-0.01250.2006-0.2903-3.22720.9730
102.10540.31712.61784.19900.64563.41420.0803-0.2985-0.11530.2516-0.2255-0.0587-0.05710.09500.15340.20950.0150-0.01910.1266-0.04080.2719-1.135616.5172-0.1250
114.56213.8486-1.48163.5449-1.82672.5744-0.13750.29440.2420-0.21730.30210.2779-0.13780.0709-0.11200.21010.00820.02790.22230.01560.2734-3.667120.2217-10.0020
124.1507-0.37893.12051.6393-0.56452.4190-0.24440.79990.4188-0.49640.0018-0.1155-0.67230.64050.26540.5085-0.11720.01470.35450.06630.28454.83598.931335.8289
133.89430.26270.67452.3796-0.03174.4046-0.29640.04650.3349-0.23930.12530.1423-0.5973-0.21750.12710.2859-0.0167-0.05900.1935-0.01320.1914-5.90625.634837.4424
142.64020.49761.94210.72160.48483.2027-0.40660.07280.4727-0.10820.05210.2168-0.8592-0.03500.31520.38880.0193-0.05650.1932-0.01240.2514-5.19179.904638.9529
151.7877-1.24800.41382.2049-0.15960.76130.04510.1710-0.1577-0.0197-0.0220-0.09690.24120.2260-0.00350.29720.00790.02100.2719-0.03220.232813.9664-15.479843.9713
163.7093-2.8561-4.58997.93306.24666.94020.19101.1706-0.6113-0.64980.0131-0.28980.31310.1037-0.10570.48900.1185-0.06840.5741-0.21880.412817.9614-29.946537.4901
172.84190.56250.71033.83464.72925.8690-0.19170.5157-0.1898-0.13630.2840-0.57180.20430.5202-0.10760.26860.04340.05290.38600.01670.393125.4280-23.181544.9150
185.31803.12891.93543.69734.25875.97990.38580.2283-0.86570.7062-0.2757-0.45621.11010.3660-0.00440.40920.0961-0.00640.27370.01770.452523.9426-28.621449.0454
191.7689-0.36450.46571.7469-0.00242.3009-0.1141-0.3528-0.11200.14510.06980.29730.0152-0.46810.07660.2201-0.00740.00210.34780.03890.1982-17.6087-8.395431.3476
202.42980.90392.35731.6966-0.62013.87830.03530.04150.0342-0.0350-0.05050.0333-0.2603-0.15950.01000.24410.0165-0.00650.2478-0.00500.2081-14.8734-0.178026.7303
211.6034-0.21940.61620.64660.27251.2265-0.0099-0.13970.05970.1085-0.01800.0682-0.0308-0.25630.02620.24430.00970.00740.33000.00990.2136-14.9160-5.748427.9013
223.1453-2.16770.44535.6341-5.06245.54990.39930.0842-0.4531-0.4353-0.24870.20381.1005-0.3008-0.16100.3970-0.0618-0.08150.2713-0.00340.2691-4.8759-23.458828.1134
233.5238-1.0867-1.91645.56121.59633.77190.1167-0.5409-0.23750.19300.2544-0.29171.00991.1413-0.43360.38560.1136-0.04720.4050-0.01360.276112.7937-32.143152.5691
241.7059-0.64300.55931.9934-0.43176.13080.0469-0.1082-0.0547-0.02440.04820.18630.67670.0073-0.09680.3455-0.0759-0.02220.23400.02200.25900.6175-24.934144.4073
253.37061.67470.63773.4949-0.98220.7430-0.08860.09230.2606-0.25920.09990.13300.24230.17240.09750.2929-0.0094-0.04800.2265-0.01570.29793.8404-20.371741.5924
261.97150.38402.21290.75750.05725.8771-0.0157-0.18010.0417-0.2382-0.07990.12660.2233-0.30150.10080.3264-0.0021-0.04040.2465-0.00790.27971.1921-26.729349.3364
271.8271-2.39541.46923.6696-2.18861.9548-0.4136-0.0240-0.25890.16220.19340.1700-0.02550.03920.17620.5614-0.1067-0.08420.29610.04660.4047-1.9668-32.660947.2047
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A2A171( CHAIN A AND RESID 2:17 )
2A18A382( CHAIN A AND RESID 18:38 )
3A39A833( CHAIN A AND RESID 39:83 )
4A84A1284( CHAIN A AND RESID 84:128 )
5A129A1495( CHAIN A AND RESID 129:149 )
6A150A1876( CHAIN A AND RESID 150:187 )
7A188A1977( CHAIN A AND RESID 188:197 )
8A198A2118( CHAIN A AND RESID 198:211 )
9B4B1579( CHAIN B AND RESID 4:157 )
10B158B17510( CHAIN B AND RESID 158:175 )
11B176B21111( CHAIN B AND RESID 176:211 )
12C1C2512( CHAIN C AND RESID 1:25 )
13C26C4813( CHAIN C AND RESID 26:48 )
14C49C9514( CHAIN C AND RESID 49:95 )
15C96C17315( CHAIN C AND RESID 96:173 )
16C174C18616( CHAIN C AND RESID 174:186 )
17C187C19917( CHAIN C AND RESID 187:199 )
18C200C21118( CHAIN C AND RESID 200:211 )
19D4D3919( CHAIN D AND RESID 4:39 )
20D40D5920( CHAIN D AND RESID 40:59 )
21D60D10621( CHAIN D AND RESID 60:106 )
22D107D11922( CHAIN D AND RESID 107:119 )
23D120D13423( CHAIN D AND RESID 120:134 )
24D135D15724( CHAIN D AND RESID 135:157 )
25D158D17525( CHAIN D AND RESID 158:175 )
26D176D20026( CHAIN D AND RESID 176:200 )
27D201D21027( CHAIN D AND RESID 201:210 )

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