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- PDB-5bzw: Crystal Structure of PCDN-27B, an antibody from the PCDN family o... -

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Basic information

Entry
Database: PDB / ID: 5bzw
TitleCrystal Structure of PCDN-27B, an antibody from the PCDN family of HIV-1 antibodies
Components
  • 2B3 HIV Antibody heavy chain
  • 2B3 HIV Antibody light chain
KeywordsIMMUNE SYSTEM / HIV / Antibody / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGarces, F. / WILSON, I.A.
CitationJournal: Immunity / Year: 2016
Title: Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch.
Authors: MacLeod, D.T. / Choi, N.M. / Briney, B. / Garces, F. / Ver, L.S. / Landais, E. / Murrell, B. / Wrin, T. / Kilembe, W. / Liang, C.H. / Ramos, A. / Bian, C.B. / Wickramasinghe, L. / Kong, L. / ...Authors: MacLeod, D.T. / Choi, N.M. / Briney, B. / Garces, F. / Ver, L.S. / Landais, E. / Murrell, B. / Wrin, T. / Kilembe, W. / Liang, C.H. / Ramos, A. / Bian, C.B. / Wickramasinghe, L. / Kong, L. / Eren, K. / Wu, C.Y. / Wong, C.H. / Kosakovsky Pond, S.L. / Wilson, I.A. / Burton, D.R. / Poignard, P.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_struct_oper_list
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2B3 HIV Antibody light chain
B: 2B3 HIV Antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1308
Polymers48,4282
Non-polymers7026
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-57 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.354, 89.354, 211.301
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-304-

SO4

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Components

#1: Antibody 2B3 HIV Antibody light chain


Mass: 23306.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EIVLTQSPGTLSLSPGERATLSCRASQSVSAKNLAWYQQKPGQTPRLLMYGVSLRNTGVP ...Details: EIVLTQSPGTLSLSPGERATLSCRASQSVSAKNLAWYQQKPGQTPRLLMYGVSLRNTGVP DRFSGSGSGTDFTLTISRLEPEDSAVYFCQQYGTSPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 2B3 HIV Antibody heavy chain


Mass: 25121.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: QVQLQQWGAGLLKPSETLSLTCAVYNESLSAFSWSWIRQFPGQGLEWIGEIDHTTSSNYN PSLKRRINISIDTSKKQFSLKLYSVTAADTAVYYCARGGRKVYHAYWSGYVNNCFDPWGQ ...Details: QVQLQQWGAGLLKPSETLSLTCAVYNESLSAFSWSWIRQFPGQGLEWIGEIDHTTSSNYN PSLKRRINISIDTSKKQFSLKLYSVTAADTAVYYCARGGRKVYHAYWSGYVNNCFDPWGQ GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCD
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 10% (v/v) ethylene glycol and 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 273.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→43.629 Å / Num. obs: 11743 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rsym value: 0.28 / Net I/σ(I): 9.8
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRH

1rrh


Resolution: 2.9→43.629 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.297 586 5.02 %
Rwork0.2333 --
obs0.2364 11669 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→43.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 39 1 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023450
X-RAY DIFFRACTIONf_angle_d0.6644692
X-RAY DIFFRACTIONf_dihedral_angle_d11.5451235
X-RAY DIFFRACTIONf_chiral_restr0.026532
X-RAY DIFFRACTIONf_plane_restr0.004601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.19180.36411540.2822692X-RAY DIFFRACTION100
3.1918-3.65340.34731560.26522669X-RAY DIFFRACTION99
3.6534-4.60220.29911280.21072797X-RAY DIFFRACTION100
4.6022-43.63370.22751480.21192925X-RAY DIFFRACTION99

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