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- PDB-4hpy: Crystal structure of RV144-elicited antibody CH59 in complex with... -

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Basic information

Entry
Database: PDB / ID: 4hpy
TitleCrystal structure of RV144-elicited antibody CH59 in complex with V2 peptide
Components
  • CH59 Fab heavy chain
  • CH59 Fab light chain
  • Envelope glycoprotein gp160
KeywordsImmune System/Viral Protein / immunoglobulin / Immune System-Viral Protein complex
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / complement activation, classical pathway / host cell endosome membrane / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell ...immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / complement activation, classical pathway / host cell endosome membrane / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / viral protein processing / virus-mediated perturbation of host defense response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular exosome / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Ig-like domain-containing protein / IGL@ protein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMcLellan, J.S. / Gorman, J. / 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 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CH59 Fab heavy chain
L: CH59 Fab light chain
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4565
Polymers49,2723
Non-polymers1842
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-32 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.888, 79.150, 127.112
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 CH59 Fab heavy chain


Mass: 23943.854 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) / References: UniProt: Q6N089*PLUS
#2: Antibody CH59 Fab light chain


Mass: 22978.287 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) / References: UniProt: Q8N5F4*PLUS
#3: Protein/peptide Envelope glycoprotein gp160


Mass: 2349.812 Da / Num. of mol.: 1 / Fragment: UNP residues 160-178 / Source method: obtained synthetically / Details: Peptide derived from HIV-1 gp120 V2 region / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9WLG7, UniProt: G9HS63*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% (w/v) PEG8000, 30% isopropanol, 0.1M imidazole pH 6.5, 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: Apr 12, 2012
RadiationMonochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 68734 / Num. obs: 68734 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.874 / Num. unique all: 3359 / % possible all: 100

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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 entry 4HPO

4hpo


Resolution: 1.5→19.892 Å / SU ML: 0.11 / σ(F): 1.36 / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 3473 5.06 %random
Rwork0.1707 ---
obs0.1715 68657 99.84 %-
all-68657 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 12 521 3868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043445
X-RAY DIFFRACTIONf_angle_d0.9984685
X-RAY DIFFRACTIONf_dihedral_angle_d12.1981236
X-RAY DIFFRACTIONf_chiral_restr0.067526
X-RAY DIFFRACTIONf_plane_restr0.005600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51880.24221100.20652493X-RAY DIFFRACTION96
1.5188-1.54050.21471390.2062571X-RAY DIFFRACTION100
1.5405-1.56350.2151260.19522555X-RAY DIFFRACTION100
1.5635-1.58790.20061230.18542587X-RAY DIFFRACTION100
1.5879-1.61390.18971390.18742630X-RAY DIFFRACTION100
1.6139-1.64180.16541220.1772541X-RAY DIFFRACTION100
1.6418-1.67160.21721380.17992640X-RAY DIFFRACTION100
1.6716-1.70370.2291430.17572522X-RAY DIFFRACTION100
1.7037-1.73850.2151300.17052606X-RAY DIFFRACTION100
1.7385-1.77630.18291190.17432593X-RAY DIFFRACTION100
1.7763-1.81760.21511300.17032614X-RAY DIFFRACTION100
1.8176-1.8630.17391450.17742582X-RAY DIFFRACTION100
1.863-1.91330.20621380.16692611X-RAY DIFFRACTION100
1.9133-1.96960.17421410.16172589X-RAY DIFFRACTION100
1.9696-2.03310.1941580.16782573X-RAY DIFFRACTION100
2.0331-2.10570.18761400.15762606X-RAY DIFFRACTION100
2.1057-2.18990.17611340.15752617X-RAY DIFFRACTION100
2.1899-2.28940.16741430.16772601X-RAY DIFFRACTION100
2.2894-2.40990.20921430.16882613X-RAY DIFFRACTION100
2.4099-2.56060.18711860.18022589X-RAY DIFFRACTION100
2.5606-2.75780.18721420.17952616X-RAY DIFFRACTION100
2.7578-3.03450.19891450.17612665X-RAY DIFFRACTION100
3.0345-3.47160.17431520.1682648X-RAY DIFFRACTION100
3.4716-4.36620.17491240.15772712X-RAY DIFFRACTION100
4.3662-19.8920.17721630.17112810X-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)
11.59050.2246-0.43381.7798-0.70721.93020.02260.0598-0.0141-0.120.0130.03080.1220.011-0.03120.0852-0.0008-0.00440.0518-0.01780.062442.634726.759165.4204
22.25030.0126-0.18291.7165-0.08611.5666-0.0318-0.10320.1786-0.0010.04020.0465-0.0531-0.1173-0.00240.10910.00880.01020.0762-0.00070.096815.438723.583493.9722
32.0802-0.2207-0.85391.17450.12431.305-0.0123-0.10440.08410.02150.0522-0.0331-0.02720.0042-0.02870.0606-0.0127-0.01350.0737-0.00880.097837.342747.685570.1887
40.8537-0.18720.28261.7641-1.05381.93680.0054-0.0577-0.05270.1738-0.0069-0.048-0.00210.07610.00130.08860.0080.0020.0708-0.00450.08225.588635.416597.693
53.8753-0.2113-0.87763.43791.22033.6766-0.04270.180.1136-0.2260.0552-0.4515-0.22870.46230.0150.0769-0.02030.00860.12570.00190.117552.434941.988661.191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 2:120 )H2 - 120
2X-RAY DIFFRACTION2( CHAIN H AND RESID 121:213 )H121 - 213
3X-RAY DIFFRACTION3( CHAIN L AND RESID 0:109 )L0 - 109
4X-RAY DIFFRACTION4( CHAIN L AND RESID 110:210 )L110 - 210
5X-RAY DIFFRACTION5( CHAIN P AND RESID 168:178 )P168 - 178

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