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- PDB-4odh: Crystal structure of human Fab CAP256-VRC26.UCA, a potent V1V2-di... -

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Basic information

Entry
Database: PDB / ID: 4odh
TitleCrystal structure of human Fab CAP256-VRC26.UCA, a potent V1V2-directed HIV-1 neutralizing antibody
Components
  • CAP256-VRC26.UCA heavy chain
  • CAP256-VRC26.UCA 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: 2.894 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 10, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CAP256-VRC26.UCA light chain
H: CAP256-VRC26.UCA heavy chain


Theoretical massNumber of molelcules
Total (without water)49,5992
Polymers49,5992
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-19 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.456, 81.194, 69.193
Angle α, β, γ (deg.)90.00, 123.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody CAP256-VRC26.UCA light chain


Mass: 22788.156 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.UCA heavy chain


Mass: 26810.764 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27% PEG8000, 0.1 M HEPES, pH 7.5, cryoprotectant: 20% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 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: 2.894→50 Å / Num. all: 7503 / Num. obs: 7503 / % possible obs: 85.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.894-32.20.3681.8182.8
3-3.12186.4
3.12-3.27186.3
3.27-3.44187.5
3.44-3.65188.9
3.65-3.94186.7
3.94-4.33186.3
4.33-4.96185.7
4.96-6.24184.7
6.24-50181.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U2S

3u2s


Resolution: 2.894→33.144 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 376 5.01 %
Rwork0.224 --
obs0.2251 7500 84.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.894→33.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 0 17 3218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043278
X-RAY DIFFRACTIONf_angle_d0.8294461
X-RAY DIFFRACTIONf_dihedral_angle_d13.6031154
X-RAY DIFFRACTIONf_chiral_restr0.045509
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.894-3.31220.3521200.28582292X-RAY DIFFRACTION83
3.3122-4.17170.26161300.23482446X-RAY DIFFRACTION88
4.1717-33.14580.19951260.19462386X-RAY DIFFRACTION84
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)
10.0057-0.0437-0.0486-0.0417-0.13710.19640.08390.0363-0.12390.0316-0.02920.09320.02160.055900.3302-0.0005-0.04780.31040.0350.315527.0888-17.6802123.0713
20.02960.04050.02290.00460.03480.0183-0.14420.0835-0.15230.01990.0618-0.15480.1168-0.1321-00.4446-0.04910.04690.39690.02040.400121.4812-14.0316129.1604
30.0271-0.0525-0.150.09690.0890.0784-0.01080.07910.10990.08690.0058-0.05270.0768-0.02200.2690.01660.01910.33890.00710.36695.9215-2.4386140.041
4-0.0168-0.0601-0.0804-0.038-0.049-0.03040.08490.1099-0.2870.00750.1527-0.37210.0014-0.125800.33060.1618-0.21310.39770.7776-0.591326.861310.9849118.5115
50.127-0.08850.18070.1206-0.14740.1520.04050.0738-0.16230.0459-0.0517-0.0162-0.2441-0.011700.42990.00910.01940.33040.07540.287427.25571.0269111.895
60.05990.00440.05460.01730.04320.03320.1504-0.01340.18430.01810.0454-0.03720.17450.071200.2889-0.0147-0.02270.37170.07080.491110.51199.4434142.8319
70.1365-0.035-0.05030.11190.0605-0.0040.0140.1321-0.07820.15030.0192-0.41430.0147-0.095700.3836-0.0329-0.01850.3924-0.01010.531614.712610.2291148.248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain L and ( resid 2 through 90 )L2 - 90
2X-RAY DIFFRACTION2chain L and ( resid 91 through 113 )L91 - 113
3X-RAY DIFFRACTION3chain L and ( resid 114 through 210 )L114 - 210
4X-RAY DIFFRACTION4chain H and ( resid 2 through 17 )H2 - 17
5X-RAY DIFFRACTION5chain H and ( resid 18 through 109 )H18 - 109
6X-RAY DIFFRACTION6chain H and ( resid 110 through 145 )H110 - 145
7X-RAY DIFFRACTION7chain H and ( resid 146 through 215 )H146 - 215

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