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

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Basic information

Entry
Database: PDB / ID: 4ybl
TitleCrystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32
Components
  • A32 antibody Fab heavy chain
  • A32 antibody light chain
  • Stabilized inner domain of clade A/E gp120
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ADCC / NON-NEUTRALIZING / ANTI-HIV-1 ENV ANTIBODY A32 / CD4I ANTIBODY / VIRAL GLYCOPROTEIN GP120 / HIV-1 ENV / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 18, 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 / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Stabilized inner domain of clade A/E gp120
H: A32 antibody Fab heavy chain
L: A32 antibody light chain
A: Stabilized inner domain of clade A/E gp120
B: A32 antibody Fab heavy chain
C: A32 antibody light chain


Theoretical massNumber of molelcules
Total (without water)126,8436
Polymers126,8436
Non-polymers00
Water0
1
G: Stabilized inner domain of clade A/E gp120
H: A32 antibody Fab heavy chain
L: A32 antibody light chain


Theoretical massNumber of molelcules
Total (without water)63,4223
Polymers63,4223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-28 kcal/mol
Surface area25100 Å2
MethodPISA
2
A: Stabilized inner domain of clade A/E gp120
B: A32 antibody Fab heavy chain
C: A32 antibody light chain


Theoretical massNumber of molelcules
Total (without water)63,4223
Polymers63,4223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-32 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.742, 208.209, 73.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe complex was purified by gel filtration prior to crystallization.

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Components

#1: Protein Stabilized inner domain of clade A/E gp120


Mass: 17236.402 Da / Num. of mol.: 2 / Mutation: V65C, S115C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: clade A/E / Cell line (production host): HEK GnT1- 293 cells / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9*PLUS
#2: Antibody A32 antibody 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 A32 antibody 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)
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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1542.9
2
3
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 18-22% PEG 6000 or 8000 0.1 M Tris-HCl pH 8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL7-111.12789
SYNCHROTRONSSRL BL12-220.97946
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 28, 2014
PSI PILATUS 6M2PIXELJan 23, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.127891
20.979461
ReflectionResolution: 3.1→50 Å / Num. all: 21415 / Num. obs: 19959 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 14.6
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 1.3 / % possible all: 96.8

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Processing

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

3tnm

4rqh
PDB Unreleased entry


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.877 / SU B: 74.752 / SU ML: 0.551 / Cross valid method: THROUGHOUT / ESU R Free: 0.629 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28937 1021 5.1 %RANDOM
Rwork0.23178 ---
obs0.2346 18913 91.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.206 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å2-0 Å2
2---0.36 Å20 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8470 0 0 0 8470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198702
X-RAY DIFFRACTIONr_bond_other_d0.0020.027928
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.93711875
X-RAY DIFFRACTIONr_angle_other_deg1.016318362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5751096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4724.84343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.248151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9271522
X-RAY DIFFRACTIONr_chiral_restr0.0910.21336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219817
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021933
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_it0.8144.194429
X-RAY DIFFRACTIONr_mcbond_other0.8144.194428
X-RAY DIFFRACTIONr_mcangle_it1.4866.2815510
X-RAY DIFFRACTIONr_mcangle_other1.4866.285511
X-RAY DIFFRACTIONr_scbond_it0.594.2614273
X-RAY DIFFRACTIONr_scbond_other0.594.264274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1036.3516366
X-RAY DIFFRACTIONr_long_range_B_refined4.0339.82634556
X-RAY DIFFRACTIONr_long_range_B_other4.0339.82634555
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 50 -
Rwork0.33 1127 -
obs--73.42 %
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)
17.6303-4.0683-1.60039.04991.1733.29540.0159-0.3678-1.04850.79450.04250.16990.67160.0474-0.05851.0777-0.0352-0.15470.73040.17090.7715-27.677326.44515.5375
21.89451.3067-0.60495.3834-1.94711.0815-0.04580.1058-0.0788-0.06720.14290.11210.1216-0.1387-0.09710.61750.006-0.02060.3743-0.02050.0239-24.37968.047-12.5945
31.46720.069-0.51495.3759-1.14341.4154-0.1138-0.1508-0.09180.2150.1857-0.0250.0462-0.0445-0.07190.67940.1134-0.01320.4714-0.06530.0319-26.367971.88493.739
47.26364.39781.35377.1271.74974.0987-0.13510.67860.1729-0.650.4051-0.1778-0.85660.3583-0.270.95650.13040.08320.62390.08351.1583-26.898747.8023-38.3246
54.013-2.31150.93845.2923-1.5691.0324-0.0973-0.38150.46160.3148-0.0046-0.1231-0.2133-0.18730.10190.5481-0.0255-0.02140.3207-0.06110.0603-17.47075.1084-22.9057
62.2009-1.31550.36055.3719-1.08061.18160.10790.24120.3616-0.242-0.0533-0.28080.01610.0102-0.05460.4871-0.07020.03950.2149-0.02220.0977-19.82422.9601-39.254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G50 - 491
2X-RAY DIFFRACTION2H1 - 214
3X-RAY DIFFRACTION3L4 - 208
4X-RAY DIFFRACTION4A45 - 491
5X-RAY DIFFRACTION5B2 - 214
6X-RAY DIFFRACTION6C4 - 208

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