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- PDB-3tnm: Crystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody -

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Basic information

Entry
Database: PDB / ID: 3tnm
TitleCrystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody
Components
  • Fab heavy chain of human anti-HIV-1 Env antibody A32
  • Fab light chain of human anti-HIV-1 Env antibody A32
KeywordsIMMUNE SYSTEM / ADCC / NON-NEUTRALIZING / ANTI-HIV-1 ENV ANTIBODY A32 / CD4i antibody / Fab / VIRAL GLYCOPROTEIN GP120 / HIV-1 Env
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWu, X. / Pazgier, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Diverse specificity and effector function among human antibodies to HIV-1 envelope glycoprotein epitopes exposed by CD4 binding.
Authors: Guan, Y. / Pazgier, M. / Sajadi, M.M. / Kamin-Lewis, R. / Al-Darmarki, S. / Flinko, R. / Lovo, E. / Wu, X. / Robinson, J.E. / Seaman, M.S. / Fouts, T.R. / Gallo, R.C. / DeVico, A.L. / Lewis, G.K.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Apr 21, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
H: Fab heavy chain of human anti-HIV-1 Env antibody A32
L: Fab light chain of human anti-HIV-1 Env antibody A32
A: Fab heavy chain of human anti-HIV-1 Env antibody A32
B: Fab light chain of human anti-HIV-1 Env antibody A32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3578
Polymers95,1924
Non-polymers1654
Water6,377354
1
H: Fab heavy chain of human anti-HIV-1 Env antibody A32
L: Fab light chain of human anti-HIV-1 Env antibody A32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7265
Polymers47,5962
Non-polymers1303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-24 kcal/mol
Surface area19080 Å2
MethodPISA
2
A: Fab heavy chain of human anti-HIV-1 Env antibody A32
B: Fab light chain of human anti-HIV-1 Env antibody A32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6313
Polymers47,5962
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-25 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.780, 71.316, 77.673
Angle α, β, γ (deg.)103.69, 104.02, 105.40
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab heavy chain of human anti-HIV-1 Env antibody A32


Mass: 24766.699 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 / Production host: Homo sapiens (human)
#2: Antibody Fab light chain of human anti-HIV-1 Env antibody A32


Mass: 22829.080 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 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 10% 2-Propanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 59060 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Rsym value: 0.107 / Net I/σ(I): 20
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2898 / Rsym value: 0.903 / % possible all: 89.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.494 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23203 3000 5.1 %RANDOM
Rwork0.18728 ---
all0.18957 3942 --
obs0.18957 56011 89.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.2 Å21.56 Å2
2---1.32 Å20.22 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 7 354 6810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226631
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9499059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66124.132242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.979151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3081522
X-RAY DIFFRACTIONr_chiral_restr0.1180.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215002
X-RAY DIFFRACTIONr_mcbond_it2.3181.54278
X-RAY DIFFRACTIONr_mcangle_it4.01726941
X-RAY DIFFRACTIONr_scbond_it4.45432353
X-RAY DIFFRACTIONr_scangle_it7.2594.52118
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 198 -
Rwork0.26 3942 -
obs--86.99 %
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)
10.1906-0.3859-0.07190.80350.12060.16110.03130.0282-0.0007-0.035-0.06580.010.0183-0.01650.03450.08610.00610.00360.0789-0.00630.0822-14.508745.30846.7657
20.0395-0.15040.1051.0449-0.27010.40920.0333-0.0251-0.0053-0.1245-0.0313-0.00090.0029-0.1002-0.0020.09930.0176-0.00930.10330.01720.0181-15.452943.977730.516
30.24070.3387-0.0150.58430.14140.2511-0.0038-0.0194-0.0276-0.0006-0.0399-0.0240.0078-0.02330.04370.0651-0.0048-0.03470.09480.00440.09352.887125.361-6.0169
40.12280.0202-0.20660.8276-0.1240.3691-0.03160.03490.01690.07860.04350.03120.0275-0.0418-0.01190.0720.0081-0.04070.11650.02380.0385-0.50326.59379.7733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 214
2X-RAY DIFFRACTION2L4 - 208
3X-RAY DIFFRACTION3A1 - 214
4X-RAY DIFFRACTION4B4 - 208

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