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- PDB-4toy: Structure of 35O22 Fab, a HIV-1 neutralizing antibody -

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Basic information

Entry
Database: PDB / ID: 4toy
TitleStructure of 35O22 Fab, a HIV-1 neutralizing antibody
Components
  • 35O22 Fab Heavy chain
  • 35O22 Fab Light chain
KeywordsIMMUNE SYSTEM / HIV-1 / antibody / Fab / neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsPancera, M. / Kwong, P.D.
CitationJournal: Nature / Year: 2014
Title: Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface.
Authors: Jinghe Huang / Byong H Kang / Marie Pancera / Jeong Hyun Lee / Tommy Tong / Yu Feng / Hiromi Imamichi / Ivelin S Georgiev / Gwo-Yu Chuang / Aliaksandr Druz / Nicole A Doria-Rose / Leo Laub / ...Authors: Jinghe Huang / Byong H Kang / Marie Pancera / Jeong Hyun Lee / Tommy Tong / Yu Feng / Hiromi Imamichi / Ivelin S Georgiev / Gwo-Yu Chuang / Aliaksandr Druz / Nicole A Doria-Rose / Leo Laub / Kwinten Sliepen / Marit J van Gils / Alba Torrents de la Peña / Ronald Derking / Per-Johan Klasse / Stephen A Migueles / Robert T Bailer / Munir Alam / Pavel Pugach / Barton F Haynes / Richard T Wyatt / Rogier W Sanders / James M Binley / Andrew B Ward / John R Mascola / Peter D Kwong / Mark Connors /
Abstract: The isolation of human monoclonal antibodies is providing important insights into the specificities that underlie broad neutralization of HIV-1 (reviewed in ref. 1). Here we report a broad and ...The isolation of human monoclonal antibodies is providing important insights into the specificities that underlie broad neutralization of HIV-1 (reviewed in ref. 1). Here we report a broad and extremely potent HIV-specific monoclonal antibody, termed 35O22, which binds a novel HIV-1 envelope glycoprotein (Env) epitope. 35O22 neutralized 62% of 181 pseudoviruses with a half-maximum inhibitory concentration (IC50) <50 μg ml(-1). The median IC50 of neutralized viruses was 0.033 μg ml(-1), among the most potent thus far described. 35O22 did not bind monomeric forms of Env tested, but did bind the trimeric BG505 SOSIP.664. Mutagenesis and a reconstruction by negative-stain electron microscopy of the Fab in complex with trimer revealed that it bound to a conserved epitope, which stretched across gp120 and gp41. The specificity of 35O22 represents a novel site of vulnerability on HIV Env, which serum analysis indicates to be commonly elicited by natural infection. Binding to this new site of vulnerability may thus be an important complement to current monoclonal-antibody-based approaches to immunotherapies, prophylaxis and vaccine design.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 35O22 Fab Heavy chain
L: 35O22 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)49,4722
Polymers49,4722
Non-polymers00
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-28 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.183, 57.183, 267.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody 35O22 Fab Heavy chain


Mass: 26153.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293 / Production host: Homo sapiens (human)
#2: Antibody 35O22 Fab Light chain


Mass: 23318.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% isopropanol, 25% PEG3350, 0.2M Ammonium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 64625 / % possible obs: 98 % / Redundancy: 11.2 % / Rsym value: 0.111 / Net I/σ(I): 20.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPI

4jpi


Resolution: 1.551→39.081 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 3278 5.08 %
Rwork0.1665 --
obs0.1673 64474 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.551→39.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 0 449 3901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053643
X-RAY DIFFRACTIONf_angle_d1.0354986
X-RAY DIFFRACTIONf_dihedral_angle_d12.2991318
X-RAY DIFFRACTIONf_chiral_restr0.036561
X-RAY DIFFRACTIONf_plane_restr0.005637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.551-1.57450.28671360.22912430X-RAY DIFFRACTION92
1.5745-1.59910.24711400.22462518X-RAY DIFFRACTION95
1.5991-1.62530.23271330.21392576X-RAY DIFFRACTION96
1.6253-1.65330.22661290.20572577X-RAY DIFFRACTION97
1.6533-1.68340.21361380.20022625X-RAY DIFFRACTION96
1.6834-1.71580.2071450.19512532X-RAY DIFFRACTION98
1.7158-1.75080.21161480.19022595X-RAY DIFFRACTION97
1.7508-1.78880.21541300.18092658X-RAY DIFFRACTION98
1.7888-1.83050.22611300.18662600X-RAY DIFFRACTION97
1.8305-1.87620.18081320.17862621X-RAY DIFFRACTION98
1.8762-1.9270.21771490.17772629X-RAY DIFFRACTION98
1.927-1.98370.21481330.17752616X-RAY DIFFRACTION98
1.9837-2.04770.16911410.16732640X-RAY DIFFRACTION98
2.0477-2.12090.19671460.16692659X-RAY DIFFRACTION98
2.1209-2.20580.21541400.16822681X-RAY DIFFRACTION98
2.2058-2.30620.20191510.1652647X-RAY DIFFRACTION99
2.3062-2.42770.1961580.16642688X-RAY DIFFRACTION99
2.4277-2.57980.21471460.17172736X-RAY DIFFRACTION100
2.5798-2.77890.18911460.17682742X-RAY DIFFRACTION100
2.7789-3.05850.17921320.17422769X-RAY DIFFRACTION100
3.0585-3.50080.17171590.15662782X-RAY DIFFRACTION100
3.5008-4.40970.14611650.14452847X-RAY DIFFRACTION100
4.4097-39.09360.15271510.15363028X-RAY DIFFRACTION100
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)
13.8004-3.2164-0.15825.26811.11081.7054-0.1372-0.19620.17090.40130.3023-0.39590.01530.1874-0.09390.24110.0224-0.06940.1554-0.03930.23281.180813.066-21.3305
25.751-3.1977-2.0095.72511.74482.2274-0.15520.02640.35040.18020.1035-0.43450.0490.1205-0.00850.1456-0.0107-0.03550.0764-0.01140.11192.6512.5525-27.9854
34.2398-1.8279-1.01714.42640.31291.35230.22140.34920.1795-0.3032-0.1972-0.1795-0.13140.016-0.01770.1728-0.0056-0.02180.11020.01380.12931.7665.6519-35.4556
43.4266-2.3128-0.35535.36740.08971.2797-0.19850.07610.39510.16130.1518-1.3645-0.03190.3641-0.10320.19970.0024-0.04830.2045-0.07980.426510.80646.4761-28.3108
57.6197-4.90970.68286.7916-0.37812.29110.23120.27450.4844-0.2193-0.1272-0.2706-0.1280.091-0.02530.1861-0.0098-0.01110.0992-0.00610.1574-3.024815.9312-28.4218
64.188-3.9997-2.43827.95324.08583.6583-0.1498-0.015-0.04410.20540.1779-0.12180.11580.17570.04430.1493-0.0042-0.00370.11440.010.14761.3091-2.8874-29.8158
70.4070.216-0.40970.0773-0.25431.5059-0.011-0.1240.17730.46560.07540.0498-0.31190.0462-0.03410.36560.03150.02150.1232-0.02410.2165-7.911312.4724-13.999
82.29381.4092-1.32519.5869-6.48887.65410.1414-0.0719-0.2235-0.24760.17280.3213-0.3287-0.5196-0.29810.34170.0898-0.0120.2532-0.00790.2184-18.31463.98828.1585
91.16770.2333-0.38071.1886-2.04754.72840.0613-0.07680.0094-0.1339-0.0069-0.1-0.57870.1353-0.0110.40910.04850.06140.1738-0.03710.1986-10.97848.9752-0.8552
101.81661.3215-2.91932.5559-3.75918.3940.3277-0.04850.07410.2207-0.01760.1808-1.3423-0.2092-0.22060.57470.0892-0.0070.3069-0.05690.2722-14.935710.581111.481
112.64341.4693-1.5192.4733-1.01962.8851-0.13680.33340.2361-0.20270.29120.28410.1185-0.3589-0.07720.1945-0.0194-0.03470.16720.02320.2159-15.3211-10.4512-33.4517
123.05640.84510.08184.1011-1.82431.457-0.0323-0.102-0.05730.2650.06810.09940.03010.10150.01960.17480.0113-0.00570.1164-0.00160.1705-5.9681-11.6939-25.3019
131.49730.9192-1.40192.0112-0.522.0318-0.00240.05380.0992-0.07-0.01890.16920.0451-0.0028-0.06250.1417-0.0004-0.01780.1278-0.00480.1564-12.1767-11.0498-30.602
140.8602-1.0791-0.71782.62691.50783.6535-0.0698-0.220.14650.36370.1531-0.0912-0.4003-0.57870.03880.35990.17010.05030.3107-0.00580.248-23.08574.4911-1.5207
151.45670.1494-0.46413.09390.76723.439-0.0706-0.13120.13040.15220.10310.4394-0.567-1.21450.07250.39090.29410.05490.5933-0.00780.2554-28.81096.9931-0.8764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'H' and (resid 26 through 43 )
3X-RAY DIFFRACTION3chain 'H' and (resid 44 through 63 )
4X-RAY DIFFRACTION4chain 'H' and (resid 64 through 75 )
5X-RAY DIFFRACTION5chain 'H' and (resid 76 through 87 )
6X-RAY DIFFRACTION6chain 'H' and (resid 88 through 100E )
7X-RAY DIFFRACTION7chain 'H' and (resid 100F through 124 )
8X-RAY DIFFRACTION8chain 'H' and (resid 125 through 143 )
9X-RAY DIFFRACTION9chain 'H' and (resid 144 through 203 )
10X-RAY DIFFRACTION10chain 'H' and (resid 204 through 224 )
11X-RAY DIFFRACTION11chain 'L' and (resid 2 through 37 )
12X-RAY DIFFRACTION12chain 'L' and (resid 38 through 61 )
13X-RAY DIFFRACTION13chain 'L' and (resid 62 through 102 )
14X-RAY DIFFRACTION14chain 'L' and (resid 103 through 129 )
15X-RAY DIFFRACTION15chain 'L' and (resid 130 through 211 )

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