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- PDB-4org: Crystal structure of human Fab CAP256-VRC26.04, a potent V1V2-dir... -

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Basic information

Entry
Database: PDB / ID: 4org
TitleCrystal structure of human Fab CAP256-VRC26.04, a potent V1V2-directed HIV-1 neutralizing antibody
Components
  • CAP256-VRC26.04 heavy chain
  • CAP256-VRC26.04 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: 3.121 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
DepositionFeb 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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

Downloads & links

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Assembly

Deposited unit
L: CAP256-VRC26.04 light chain
H: CAP256-VRC26.04 heavy chain
B: CAP256-VRC26.04 light chain
A: CAP256-VRC26.04 heavy chain
D: CAP256-VRC26.04 light chain
C: CAP256-VRC26.04 heavy chain
F: CAP256-VRC26.04 light chain
E: CAP256-VRC26.04 heavy chain


Theoretical massNumber of molelcules
Total (without water)203,7198
Polymers203,7198
Non-polymers00
Water00
1
L: CAP256-VRC26.04 light chain
H: CAP256-VRC26.04 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,9302
Polymers50,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-24 kcal/mol
Surface area21580 Å2
MethodPISA
2
B: CAP256-VRC26.04 light chain
A: CAP256-VRC26.04 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,9302
Polymers50,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-22 kcal/mol
Surface area20890 Å2
MethodPISA
3
D: CAP256-VRC26.04 light chain
C: CAP256-VRC26.04 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,9302
Polymers50,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area21690 Å2
MethodPISA
4
F: CAP256-VRC26.04 light chain
E: CAP256-VRC26.04 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,9302
Polymers50,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.023, 85.471, 103.274
Angle α, β, γ (deg.)97.90, 107.72, 91.67
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
CAP256-VRC26.04 light chain


Mass: 22755.232 Da / Num. of mol.: 4 / 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-VRC26.04 heavy chain


Mass: 28174.617 Da / Num. of mol.: 4 / 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)

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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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 14% PEG3350, 25% isopropanol, 0.1 M Tris, pH 8.0, cryoprotectant: 20% ethylene glycol, 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: 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: 3.121→97.204 Å / Num. all: 38926 / Num. obs: 36109 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.121-3.21.80.3911.841550179.6
3.2-3.261.80.381.91614183.8

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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 4OCW

4ocw


Resolution: 3.121→35.629 Å / SU ML: 0.43 / σ(F): 1.96 / Phase error: 43.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 1808 5.01 %RANDOM
Rwork0.2748 ---
obs0.2755 36066 92.71 %-
all-36066 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.121→35.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13397 0 0 0 13397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313741
X-RAY DIFFRACTIONf_angle_d0.72618695
X-RAY DIFFRACTIONf_dihedral_angle_d10.6244870
X-RAY DIFFRACTIONf_chiral_restr0.0272107
X-RAY DIFFRACTIONf_plane_restr0.0042384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.121-3.20540.4286960.38841817X-RAY DIFFRACTION64
3.2054-3.29960.40621280.36142458X-RAY DIFFRACTION87
3.2996-3.4060.37591390.35262661X-RAY DIFFRACTION92
3.406-3.52770.3451510.32642681X-RAY DIFFRACTION96
3.5277-3.66880.34561440.31962782X-RAY DIFFRACTION97
3.6688-3.83560.32011380.30432768X-RAY DIFFRACTION98
3.8356-4.03750.32041560.29542809X-RAY DIFFRACTION98
4.0375-4.29010.32091430.26862775X-RAY DIFFRACTION98
4.2901-4.62070.24181490.24552752X-RAY DIFFRACTION97
4.6207-5.08450.23561430.23222765X-RAY DIFFRACTION98
5.0845-5.81750.24961460.24882806X-RAY DIFFRACTION98
5.8175-7.31890.25531490.25442783X-RAY DIFFRACTION98
7.3189-35.63140.21021260.21272401X-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)
10.01860.01260.0064-0.00050.00110.03030.12020.07850.0796-0.02210.099-0.0128-0.18080.0817-00.4831-0.02-0.07050.50860.01920.354312.7915-31.4154-10.6714
20.04810.01510.0126-0.0170.0518-0.0094-0.08630.04740.0992-0.1183-0.08750.0621-0.0246-0.039-0-0.1706-0.23010.0036-0.02580.15230.12682.769-44.859-34.7613
30.0324-0.02550.00870.0112-0.00290.01960.0410.21770.09050.0877-0.02850.0354-0.1672-0.1039-00.46080.0432-0.04880.2351-0.09770.3783-8.1032-24.0975-3.5649
40.0241-0.00280.00650.00390.003-0.00890.0324-0.1722-0.18820.0307-0.1082-0.00260.0870.088800.2012-0.42160.07530.1448-0.18840.2998-8.183-57.8542-33.6246
50.02750.00710.00590.00810.01760.02420.0150.05110.0942-0.0173-0.0143-0.0878-0.13950.074100.3864-0.0176-0.03820.2873-0.09490.355831.3494-39.37838.0137
60.03230.02850.00120.00960.03580.01940.0046-0.00210.1183-0.09550.11960.0542-0.00870.0277-00.02650.22240.14830.565-0.2050.325521.2047-52.500413.8046
70.01380.00860.00080.00010.00060.0322-0.03280.1037-0.03970.0832-0.04070.0371-0.2128-0.1169-00.31650.075-0.04020.4986-0.05550.296310.5652-32.669444.2912
80.01270.00090.00940.0056-0.0148-0.0095-0.0201-0.0511-0.0035-0.0233-0.0581-0.0060.2283-0.1059-0-0.36290.4298-0.1860.07410.19010.136110.4767-65.518414.7968
90.0337-0.00450.00570.01430.01570.0202-0.02760.0258-0.0607-0.01140.0280.02280.06330.0851-00.5568-0.17190.1250.418-0.11630.44-5.34976.2218-14.7783
100.04720.00790.0044-0.00070.03940.0083-0.0508-0.0217-0.04020.05810.04530.0257-0.03390.0772-00.1156-0.07720.15590.3364-0.20870.3627-15.391517.707510.8622
110.03120.0020.02040.00270.00560.01970.0478-0.02380.05470.0045-0.06410.10030.0144-0.1167-00.4139-0.0794-0.0260.3401-0.14280.4128-25.8885-3.2839-19.518
120.0050.00080.001-0.0107-0.0106-0.00020.05230.1480.0278-0.099-0.01040.0348-0.01080.0304-0-0.5135-0.37350.2898-0.06310.14860.2297-26.157830.18479.9456
130.0292-0.01510.02940.00840.00220.02660.0250.03680.0456-0.07450.0534-0.02710.09020.0786-00.29310.0527-0.05830.23670.11070.321212.92-1.340633.8668
140.0414-0.02010.00630.01020.01580.0083-0.0124-0.0892-0.10680.14260.15240.02130.0081-0.07500.15010.0357-0.00440.14610.25740.12762.821510.216559.6768
150.03750.0181-0.00070.01390.0122-0.0107-0.0561-0.0907-0.10580.0119-0.08650.2168-0.03720.026700.39650.00990.08920.3729-0.13680.4356-7.5994-11.133429.1049
160.0174-0.012-0.001-0.00760.01170.01450.02450.12230.2502-0.1807-0.0267-0.095-0.13710.074700.1237-0.0083-0.08120.3671-0.08340.282-8.149222.546158.3491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain L and ( resid 3 through 109 )L3 - 109
2X-RAY DIFFRACTION2chain L and ( resid 110 through 208 )L110 - 208
3X-RAY DIFFRACTION3chain H and ( resid 2 through 113 )H2 - 113
4X-RAY DIFFRACTION4chain H and ( resid 114 through 213 )H114 - 213
5X-RAY DIFFRACTION5chain B and ( resid 3 through 109 )B3 - 109
6X-RAY DIFFRACTION6chain B and ( resid 110 through 208 )B110 - 208
7X-RAY DIFFRACTION7chain A and ( resid 2 through 113 )A2 - 113
8X-RAY DIFFRACTION8chain A and ( resid 114 through 213 )A114 - 213
9X-RAY DIFFRACTION9chain D and ( resid 3 through 109 )D3 - 109
10X-RAY DIFFRACTION10chain D and ( resid 110 through 209 )D110 - 209
11X-RAY DIFFRACTION11chain C and ( resid 2 through 113 )C2 - 113
12X-RAY DIFFRACTION12chain C and ( resid 114 through 215 )C114 - 215
13X-RAY DIFFRACTION13chain F and ( resid 3 through 109 )F3 - 109
14X-RAY DIFFRACTION14chain F and ( resid 110 through 210 )F110 - 210
15X-RAY DIFFRACTION15chain E and ( resid 2 through 113 )E2 - 113
16X-RAY DIFFRACTION16chain E and ( resid 114 through 215 )E114 - 215

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