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- PDB-4hpo: Crystal structure of RV144-elicited antibody CH58 in complex with... -

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Basic information

Entry
Database: PDB / ID: 4hpo
TitleCrystal structure of RV144-elicited antibody CH58 in complex with V2 peptide
Components
  • CH58 Fab heavy chain
  • CH58 Fab light chain
  • Envelope glycoprotein gp160
KeywordsImmune System/Viral Protein / Immunoglobulin / Immune System-Viral Protein complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.694 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 27, 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
H: CH58 Fab heavy chain
L: CH58 Fab light chain
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9074
Polymers50,5393
Non-polymers3671
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-24 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.594, 75.804, 54.688
Angle α, β, γ (deg.)90.00, 111.99, 90.00
Int Tables number5
Space group name H-MC121

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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: Protein/peptide Envelope glycoprotein gp160


Mass: 2349.812 Da / Num. of mol.: 1 / Fragment: UNP residues 160-178 / Source method: obtained synthetically / Details: peptide from HIV-1 V2 region / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9WLG7, UniProt: G9HS63*PLUS
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% (w/v) PEG 8000, 2% (v/v) MPD, 0.1 M 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: Mar 10, 2012
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.694→50 Å / Num. all: 59036 / Num. obs: 53546 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.694→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.88 / % possible all: 56.1

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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: 1.694→24.806 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 2654 4.97 %
Rwork0.1854 --
obs0.1866 53364 90.22 %
all-59149 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.694→24.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 24 403 3833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073534
X-RAY DIFFRACTIONf_angle_d1.1054813
X-RAY DIFFRACTIONf_dihedral_angle_d14.7581265
X-RAY DIFFRACTIONf_chiral_restr0.077539
X-RAY DIFFRACTIONf_plane_restr0.005604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.694-1.7250.3461850.26121564X-RAY DIFFRACTION53
1.725-1.75820.2445920.25241795X-RAY DIFFRACTION61
1.7582-1.7940.33471120.24942080X-RAY DIFFRACTION71
1.794-1.8330.29581270.23732327X-RAY DIFFRACTION79
1.833-1.87570.24691290.23762507X-RAY DIFFRACTION85
1.8757-1.92250.25431130.2422599X-RAY DIFFRACTION88
1.9225-1.97450.28521540.22922763X-RAY DIFFRACTION94
1.9745-2.03260.24051470.2092868X-RAY DIFFRACTION97
2.0326-2.09810.22061510.19722881X-RAY DIFFRACTION97
2.0981-2.17310.21151370.19322896X-RAY DIFFRACTION98
2.1731-2.260.27491470.20872868X-RAY DIFFRACTION98
2.26-2.36280.24411460.21592933X-RAY DIFFRACTION99
2.3628-2.48730.22281590.20142937X-RAY DIFFRACTION99
2.4873-2.6430.23281440.20452932X-RAY DIFFRACTION99
2.643-2.84680.21871650.20362963X-RAY DIFFRACTION99
2.8468-3.13270.23631680.19672919X-RAY DIFFRACTION100
3.1327-3.58490.20141670.17872963X-RAY DIFFRACTION100
3.5849-4.51220.17571660.14852961X-RAY DIFFRACTION100
4.5122-24.8090.15951450.15372954X-RAY DIFFRACTION97
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)
13.39130.022-0.96121.0888-0.00082.63770.0831.51860.425-0.23580.04350.1588-0.2349-0.54550.01290.30270.0348-0.01960.68530.11960.2582-16.30336.9915-20.4873
27.69421.13032.12114.13511.01093.8808-0.0711.14240.13010.00910.13020.49750.04670.1812-0.00250.22280.0070.00560.3602-0.02240.5055-54.51196.4228-3.4022
33.4642-0.0368-0.38892.08550.43771.4297-0.02210.0234-0.22290.0032-0.00730.00340.006-0.09850.02720.1933-0.00410.00170.15030.00450.1673-14.82-1.2705-0.6103
41.83611.29470.27971.97110.94242.22370.3120.3235-1.5384-0.0673-0.0199-0.00250.47880.0883-0.29570.41640.0256-0.16180.3384-0.19791.1598-45.6951-6.99121.1493
55.09651.9463-1.54548.0313-4.68647.843-0.02431.0185-0.1833-0.6808-0.2132-0.32580.25230.49560.33660.24750.01540.0810.4756-0.10950.27680.1518-2.2914-18.1328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:124 )H1 - 124
2X-RAY DIFFRACTION2( CHAIN H AND RESID 125:213 )H125 - 213
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:112 )L1 - 112
4X-RAY DIFFRACTION4( CHAIN L AND RESID 113:209 )L113 - 209
5X-RAY DIFFRACTION5( CHAIN P AND ( RESID 167:181 OR RESID 201:222 ) )P167 - 181
6X-RAY DIFFRACTION5( CHAIN P AND ( RESID 167:181 OR RESID 201:222 ) )P201 - 222

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