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- PDB-4od3: Crystal structure of human Fab CAP256-VRC26.07, a potent V1V2-dir... -

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Basic information

Entry
Database: PDB / ID: 4od3
TitleCrystal structure of human Fab CAP256-VRC26.07, a potent V1V2-directed HIV-1 neutralizing antibody
Components
  • CAP256-VRC26.07 heavy chain
  • CAP256-VRC26.07 light chain
KeywordsIMMUNE SYSTEM / Fab / HIV-1 / V1V2 / CAP256 / VRC26
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.616 Å
AuthorsGorman, J. / Doria-Rose, N.A. / Schramm, C.A. / Moore, P.L. / Mascola, J.R. / Shapiro, L. / Morris, L. / Kwong, P.D.
CitationJournal: Nature / Year: 2014
Title: Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies.
Authors: Nicole A Doria-Rose / Chaim A Schramm / Jason Gorman / Penny L Moore / Jinal N Bhiman / Brandon J DeKosky / Michael J Ernandes / Ivelin S Georgiev / Helen J Kim / Marie Pancera / Ryan P ...Authors: Nicole A Doria-Rose / Chaim A Schramm / Jason Gorman / Penny L Moore / Jinal N Bhiman / Brandon J DeKosky / Michael J Ernandes / Ivelin S Georgiev / Helen J Kim / Marie Pancera / Ryan P Staupe / Han R Altae-Tran / Robert T Bailer / Ema T Crooks / Albert Cupo / Aliaksandr Druz / Nigel J Garrett / Kam H Hoi / Rui Kong / Mark K Louder / Nancy S Longo / Krisha McKee / Molati Nonyane / Sijy O'Dell / Ryan S Roark / Rebecca S Rudicell / Stephen D Schmidt / Daniel J Sheward / Cinque Soto / Constantinos Kurt Wibmer / Yongping Yang / Zhenhai Zhang / / James C Mullikin / James M Binley / Rogier W Sanders / Ian A Wilson / John P Moore / Andrew B Ward / George Georgiou / Carolyn Williamson / Salim S Abdool Karim / Lynn Morris / Peter D Kwong / Lawrence Shapiro / John R Mascola /
Abstract: Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental ...Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CAP256-VRC26.07 light chain
H: CAP256-VRC26.07 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4355
Polymers51,1092
Non-polymers3263
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-51 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 87.268, 224.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11L-302-

ZN

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Components

#1: Antibody CAP256-VRC26.07 light chain


Mass: 22989.518 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody CAP256-VRC26.07 heavy chain


Mass: 28119.502 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4% PEG8000, 0.1 M zinc acetate, 0.1 M MES, pH 6, cryoprotectant: 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2013
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.616→50 Å / Num. all: 19943 / Num. obs: 19943 / % possible obs: 93.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.616-2.643.91.6548153
2.64-2.6942690165.9
2.69-2.744.12.1781176.2
2.74-2.84.52.3911185.5
2.8-2.8653.1999196.4
2.86-2.935.94.61046198.9
2.93-36.551037199.8
3-3.0876.510521100
3.08-3.177.37.810641100
3.17-3.287.49.210231100
3.28-3.397.410.710501100
3.39-3.537.310.910771100
3.53-3.697.311.810541100
3.69-3.887.314.110571100
3.88-4.137.215.110781100
4.13-4.447.215.710591100
4.44-4.897.116.210611100
4.89-5.67.216.410921100
5.6-7.057.117.610991100
7.05-406.612.91165199.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U2S
Resolution: 2.616→39.904 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 997 5.01 %
Rwork0.221 --
obs0.2222 19901 93.1 %
all-19901 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.616→39.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 14 16 3391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053459
X-RAY DIFFRACTIONf_angle_d1.0144704
X-RAY DIFFRACTIONf_dihedral_angle_d13.5141236
X-RAY DIFFRACTIONf_chiral_restr0.058526
X-RAY DIFFRACTIONf_plane_restr0.004601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.616-2.75420.3734910.33191725X-RAY DIFFRACTION61
2.7542-2.92680.33551380.31642609X-RAY DIFFRACTION91
2.9268-3.15260.33361500.29562841X-RAY DIFFRACTION100
3.1526-3.46970.27291510.2492870X-RAY DIFFRACTION100
3.4697-3.97140.25481520.22752887X-RAY DIFFRACTION100
3.9714-5.0020.1981540.17522930X-RAY DIFFRACTION100
5.002-39.90910.21831610.20173042X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.05120.227-0.50851.202-0.59350.89860.06030.0816-0.06970.0018-0.0495-0.24060.08630.3546-00.66730.0134-0.0740.6456-0.00110.54956.7008-19.148-22.7726
20.5844-0.03810.04961.3984-0.5781.4707-0.02090.03240.1087-0.02940.0242-0.15090.017-0.063400.47770.01960.00730.4586-0.02730.4936-0.9313-17.1093-50.8036
30.8934-0.45390.13771.18960.52111.7518-0.0031-0.1006-0.23330.1916-0.02280.64440.008-0.066600.6015-0.09130.05080.64440.0210.7027-13.4248-14.8392-15.9969
42.56310.7577-0.04810.5493-0.67340.8119-0.15860.0417-0.66290.0147-0.0285-0.26440.0179-0.1796-00.5111-0.00140.02570.5208-0.02630.6787-13.3922-25.9559-56.1564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain L and ( resid 2 through 103 )L2 - 103
2X-RAY DIFFRACTION2chain L and ( resid 104 through 209 )L104 - 209
3X-RAY DIFFRACTION3chain H and ( resid 2 through 109 )H2 - 109
4X-RAY DIFFRACTION4chain H and ( resid 110 through 215 )H110 - 215

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