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- PDB-4yc2: Crystal structure of the stabilized inner domain of clade A/E HIV... -

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Basic information

Entry
Database: PDB / ID: 4yc2
TitleCrystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 from E. coli in complex with the antibody A32.
Components
  • The antibody A32 Fab heavy chain.
  • The antibody A32 Fab light chain.
  • The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ADCC / NON-NEUTRALIZING / ANTI-HIV-1 ENV ANTIBODY A32 / CD4I ANTIBODY / CLADE A/E 93TH057 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1033109 United States
CitationJournal: Structure / Year: 2016
Title: Paring Down HIV Env: Design and Crystal Structure of a Stabilized Inner Domain of HIV-1 gp120 Displaying a Major ADCC Target of the A32 Region.
Authors: Tolbert, W.D. / Gohain, N. / Veillette, M. / Chapleau, J.P. / Orlandi, C. / Visciano, M.L. / Ebadi, M. / DeVico, A.L. / Fouts, T.R. / Finzi, A. / Lewis, G.K. / Pazgier, M.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Sep 27, 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 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli
H: The antibody A32 Fab heavy chain.
L: The antibody A32 Fab light chain.
A: The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli
B: The antibody A32 Fab heavy chain.
C: The antibody A32 Fab light chain.


Theoretical massNumber of molelcules
Total (without water)127,1326
Polymers127,1326
Non-polymers00
Water724
1
G: The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli
H: The antibody A32 Fab heavy chain.
L: The antibody A32 Fab light chain.


Theoretical massNumber of molelcules
Total (without water)63,5663
Polymers63,5663
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-29 kcal/mol
Surface area25590 Å2
MethodPISA
2
A: The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli
B: The antibody A32 Fab heavy chain.
C: The antibody A32 Fab light chain.


Theoretical massNumber of molelcules
Total (without water)63,5663
Polymers63,5663
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-29 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.801, 211.800, 72.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsComplexes were purified by gel filtration prior to crystallization

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Components

#1: Protein The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli


Mass: 17380.535 Da / Num. of mol.: 2 / Mutation: V65C, S115C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Variant: clade A/E / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE) / References: UniProt: A0A0M3KKW9*PLUS
#2: Antibody The antibody A32 Fab heavy chain.


Mass: 23991.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 cells / Production host: Homo sapiens (human)
#3: Antibody The antibody A32 Fab light chain.


Mass: 22193.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 cells / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe sequence of the clade A/E gp120 is based on the HIV-1 clade A/E gp120 sequence in PDB ID 3TGT. ...The sequence of the clade A/E gp120 is based on the HIV-1 clade A/E gp120 sequence in PDB ID 3TGT. The sequence was engineered to remove the outer domain of gp120 and consists of the N-terminal sequence plus some of the C-terminal sequence. The numbering in the PDB file is consistent with 3TGT and 4H8W and is based on the Hxbc2 gp120 sequence which serves as the reference sequence for most gp120 structures.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 18-22% PEG 6000 or PEG8000 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 23714 / Num. obs: 20655 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHENIXrefinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TNM and 4RQH

3tnm

4rqh
PDB Unreleased entry


Resolution: 3.02→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 72.5 / SU ML: 0.556 / Cross valid method: THROUGHOUT / ESU R Free: 0.616 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28774 1087 5.3 %RANDOM
Rwork0.22724 ---
obs0.23034 19540 86.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.657 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0 Å2-0 Å2
2--0.19 Å2-0 Å2
3---1.34 Å2
Refinement stepCycle: 1 / Resolution: 3.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8600 0 0 4 8604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198839
X-RAY DIFFRACTIONr_bond_other_d0.0030.028041
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.93712062
X-RAY DIFFRACTIONr_angle_other_deg1.015318633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2951114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78724.842349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.925151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9941522
X-RAY DIFFRACTIONr_chiral_restr0.0810.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219980
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021966
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9176.2774495
X-RAY DIFFRACTIONr_mcbond_other0.9186.2784494
X-RAY DIFFRACTIONr_mcangle_it1.729.4035596
X-RAY DIFFRACTIONr_mcangle_other1.729.4025597
X-RAY DIFFRACTIONr_scbond_it0.4976.4034344
X-RAY DIFFRACTIONr_scbond_other0.4976.4034345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0179.5556467
X-RAY DIFFRACTIONr_long_range_B_refined4.98459.96535260
X-RAY DIFFRACTIONr_long_range_B_other4.98459.96635259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.02→3.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 78 -
Rwork0.331 1228 -
obs--76.42 %
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)
12.7938-2.7963-1.13324.82420.87851.4595-0.0725-0.1241-0.49590.52470.23090.18440.1566-0.009-0.15840.32080.0339-0.06040.17180.05640.3333-25.058828.07175.3714
20.69251.0996-0.35063.1895-0.7390.4733-0.00630.1004-0.0531-0.05080.0057-0.0444-0.031-0.09240.00060.29290.0076-0.01310.3322-0.03170.0116-23.640170.0257-12.9978
30.06680.24180.01322.7845-0.10290.3193-0.00660.1186-0.02740.24830.13810.0356-0.0674-0.0216-0.13150.37860.10840.01330.3275-0.05360.0629-25.332173.89823.052
45.99073.65450.73684.36821.55711.05460.06080.32310.8922-0.12710.22910.057-0.2633-0.2472-0.28990.27220.12410.05990.28410.25110.5332-27.573947.4988-38.6143
51.3557-1.57870.13942.9585-0.78880.4317-0.07990.15720.04260.3224-0.0349-0.1849-0.0645-0.0920.11480.2881-0.0112-0.03870.27680.02580.0562-17.37635.4099-22.3773
60.67-0.3928-0.18862.4122-0.82460.532-0.05130.37590.02450.02760.0529-0.10520.0175-0.1296-0.00150.3388-0.0417-0.01220.3913-0.01890.0217-19.87722.8109-38.5408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G45 - 491
2X-RAY DIFFRACTION2H1 - 214
3X-RAY DIFFRACTION3L4 - 208
4X-RAY DIFFRACTION4A45 - 491
5X-RAY DIFFRACTION5B1 - 214
6X-RAY DIFFRACTION6C4 - 208

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