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- PDB-4hqq: Crystal structure of RV144-elicited antibody CH58 -

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Basic information

Entry
Database: PDB / ID: 4hqq
TitleCrystal structure of RV144-elicited antibody CH58
Components
  • CH58 Fab heavy chain
  • CH58 Fab light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMcLellan, J.S. / Haynes, B.F. / Kwong, P.D.
CitationJournal: Immunity / Year: 2013
Title: Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2.
Authors: Liao, H.X. / Bonsignori, M. / Alam, S.M. / McLellan, J.S. / Tomaras, G.D. / Moody, M.A. / Kozink, D.M. / Hwang, K.K. / Chen, X. / Tsao, C.Y. / Liu, P. / Lu, X. / Parks, R.J. / Montefiori, D. ...Authors: Liao, H.X. / Bonsignori, M. / Alam, S.M. / McLellan, J.S. / Tomaras, G.D. / Moody, M.A. / Kozink, D.M. / Hwang, K.K. / Chen, X. / Tsao, C.Y. / Liu, P. / Lu, X. / Parks, R.J. / Montefiori, D.C. / Ferrari, G. / Pollara, J. / Rao, M. / Peachman, K.K. / Santra, S. / Letvin, N.L. / Karasavvas, N. / Yang, Z.Y. / Dai, K. / Pancera, M. / Gorman, J. / Wiehe, K. / Nicely, N.I. / Rerks-Ngarm, S. / Nitayaphan, S. / Kaewkungwal, J. / Pitisuttithum, P. / Tartaglia, J. / Sinangil, F. / Kim, J.H. / Michael, N.L. / Kepler, T.B. / Kwong, P.D. / Mascola, J.R. / Nabel, G.J. / Pinter, A. / Zolla-Pazner, S. / Haynes, B.F.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: CH58 Fab heavy chain
L: CH58 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,1892
Polymers48,1892
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-24 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.949, 70.440, 135.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody CH58 Fab heavy chain


Mass: 25035.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody CH58 Fab light chain


Mass: 23154.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 38% (w/v) PEG 8000, 0.2 M NaCl, 0.1 M sodium phosphate-citrate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2012
RadiationMonochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 24300 / Num. obs: 23741 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.506 / % possible all: 82.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3H0T 3UJJ

3h0t

3ujj


Resolution: 2.4→25.843 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1219 5.15 %random
Rwork0.1831 ---
obs0.1852 23681 97.51 %-
all-24286 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→25.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 0 191 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043320
X-RAY DIFFRACTIONf_angle_d0.8714521
X-RAY DIFFRACTIONf_dihedral_angle_d12.3311174
X-RAY DIFFRACTIONf_chiral_restr0.059504
X-RAY DIFFRACTIONf_plane_restr0.004573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49620.3268980.24872158X-RAY DIFFRACTION86
2.4962-2.60970.25721430.2352404X-RAY DIFFRACTION95
2.6097-2.74710.27951200.23062486X-RAY DIFFRACTION99
2.7471-2.9190.26011390.22432514X-RAY DIFFRACTION99
2.919-3.14410.24851290.21472544X-RAY DIFFRACTION99
3.1441-3.45980.25491340.18822521X-RAY DIFFRACTION100
3.4598-3.95890.20621690.1812536X-RAY DIFFRACTION100
3.9589-4.98190.1981450.14092591X-RAY DIFFRACTION100
4.9819-25.8430.20241420.16822708X-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)
13.4177-0.84312.38681.5811-0.18832.6847-0.11790.06470.0634-0.07450.0185-0.1001-0.13510.07230.09110.2176-0.01010.03020.2865-0.01430.273-10.3777-9.928-2.4758
23.5504-1.9739-3.2334.58173.87988.18420.0505-0.1011-0.11690.4335-0.07870.2182-0.062-0.29150.01690.37380.04260.00110.2884-0.02260.317-5.2656-3.861233.186
34.32870.31561.89515.6005-0.06994.4165-0.4749-0.00140.6216-0.32030.2651-0.1478-0.9821-0.10880.12090.5724-0.0021-0.08340.31810.01820.4615-11.532412.5358-4.4752
45.3276-0.51151.62097.68720.92926.84370.10130.032-0.174-0.57410.0012-0.3747-0.55270.2712-0.07820.4956-0.03590.0640.274-0.03710.30666.30587.915330.0419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:121 )H1 - 121
2X-RAY DIFFRACTION2( CHAIN H AND RESID 122:214 )H122 - 214
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:112 )L1 - 112
4X-RAY DIFFRACTION4( CHAIN L AND RESID 113:208 )L113 - 208

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