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- PDB-4fz8: Crystal structure of C11 Fab, an ADCC mediating anti-HIV-1 antibody. -

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Basic information

Entry
Database: PDB / ID: 4fz8
TitleCrystal structure of C11 Fab, an ADCC mediating anti-HIV-1 antibody.
Components
  • FAB heavy chain of human ANTI-HIV-1 ENV ANTIBODY C11
  • FAB light chain of human ANTI-HIV-1 ENV ANTIBODY C11
KeywordsIMMUNE SYSTEM / ADCC / ANTI-HIV-1 ENV ANTIBODY C11 / CD4I ANTIBODY / FAB / VIRAL GLYCOPROTEIN GP120 / HIV-1 ENV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsWu, X. / Tolbert, W.D. / Pazgier, M.
CitationJournal: Mbio / Year: 2020
Title: Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial.
Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. ...Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. / Lewis, G.K. / Pazgier, M.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 19, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name ..._chem_comp.pdbx_synonyms / _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
Revision 1.4Sep 13, 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 1.5Nov 6, 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: FAB heavy chain of human ANTI-HIV-1 ENV ANTIBODY C11
L: FAB light chain of human ANTI-HIV-1 ENV ANTIBODY C11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4004
Polymers49,1142
Non-polymers2872
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-53 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.547, 56.011, 70.708
Angle α, β, γ (deg.)90.00, 106.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody FAB heavy chain of human ANTI-HIV-1 ENV ANTIBODY C11


Mass: 25403.332 Da / Num. of mol.: 1
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 C11


Mass: 23710.502 Da / Num. of mol.: 1
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 294 K / pH: 7.5
Details: 0.14 M sodium citrate, 0.07 M HEPES sodium pH 7.5, 14% isopropanol, and 30% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2012 / Details: K-B FOCUSING MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 14023 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 16.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.3 / % possible all: 87.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TNN

3tnn


Resolution: 2.66→34.35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 53.222 / SU ML: 0.467 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3126 708 5.1 %RANDOM
Rwork0.2528 ---
obs0.2558 13286 95.54 %-
all-13304 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.46 Å2
Baniso -1Baniso -2Baniso -3
1--10.27 Å2-0 Å2-3.01 Å2
2--21.4 Å2-0 Å2
3----8.63 Å2
Refinement stepCycle: LAST / Resolution: 2.66→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 15 10 3348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193418
X-RAY DIFFRACTIONr_bond_other_d0.0030.023146
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9584651
X-RAY DIFFRACTIONr_angle_other_deg1.0613.0027249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4225434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48724.161137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.41615538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.421515
X-RAY DIFFRACTIONr_chiral_restr0.1110.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213892
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02777
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_it4.0751.52172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.52923504
X-RAY DIFFRACTIONr_scbond_it4.86831251
X-RAY DIFFRACTIONr_scangle_it6.3094.51153
X-RAY DIFFRACTIONr_rigid_bond_restr5.88936562
X-RAY DIFFRACTIONr_sphericity_free53
X-RAY DIFFRACTIONr_sphericity_bonded36.20456491
LS refinement shellResolution: 2.66→2.732 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.568 43 -
Rwork0.475 697 -
obs--69.35 %
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)
11.9072-0.11990.41690.14340.61163.0989-0.07960.1980.1035-0.011-0.0101-0.0064-0.18990.02740.08960.8547-0.0671-0.07510.02530.03450.7658-13.5772-14.6561-11.6408
20.9827-0.3595-0.0120.42750.5691.2371-0.0934-0.5215-0.2812-0.1380.1793-0.037-0.0841-0.0766-0.08590.83010.0031-0.02470.30160.05240.8098-17.7301-25.49973.3106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 215
2X-RAY DIFFRACTION2L1 - 211

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