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- PDB-6mu3: Anti-HIV-1 Fab 2G12 + Man7 re-refinement -

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Basic information

Entry
Database: PDB / ID: 6mu3
TitleAnti-HIV-1 Fab 2G12 + Man7 re-refinement
Components
  • Fab 2G12, heavy chain
  • Fab 2G12, light chain
KeywordsIMMUNE SYSTEM / antibody / carbohydrate / HIV-1
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Immunoglobulin kappa light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.327 Å
AuthorsWilson, I.A. / Calarese, D.A. / Stanfield, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM46192 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2005
Title: Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12.
Authors: Calarese, D.A. / Lee, H.K. / Huang, C.Y. / Best, M.D. / Astronomo, R.D. / Stanfield, R.L. / Katinger, H. / Burton, D.R. / Wong, C.H. / Wilson, I.A.
History
DepositionOct 22, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionOct 31, 2018ID: 1ZLV
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 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
L: Fab 2G12, light chain
H: Fab 2G12, heavy chain
K: Fab 2G12, light chain
M: Fab 2G12, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6916
Polymers94,3574
Non-polymers1,3332
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-24 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.822, 131.089, 169.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab 2G12, light chain


Mass: 23245.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX7
#2: Antibody Fab 2G12, heavy chain


Mass: 23932.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2/a3-b1_b2-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 20% Peg 4000, 0.2M sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.327→50 Å / Num. obs: 43875 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 47.2 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.65 / Net I/σ(I): 45.1
Reflection shellResolution: 2.327→2.37 Å / Redundancy: 6 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2158 / Χ2: 0.96 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OP3

1op3
PDB Unreleased entry


Resolution: 2.327→40.426 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.91
RfactorNum. reflection% reflection
Rfree0.2345 2192 5.01 %
Rwork0.2011 --
obs0.2028 43788 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.327→40.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 90 82 6664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046765
X-RAY DIFFRACTIONf_angle_d0.7489224
X-RAY DIFFRACTIONf_dihedral_angle_d14.2734066
X-RAY DIFFRACTIONf_chiral_restr0.0481076
X-RAY DIFFRACTIONf_plane_restr0.0051155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3266-2.37720.32131240.28052512X-RAY DIFFRACTION96
2.3772-2.43250.3531460.27572536X-RAY DIFFRACTION100
2.4325-2.49330.31181310.26642603X-RAY DIFFRACTION100
2.4933-2.56070.34581370.27142532X-RAY DIFFRACTION100
2.5607-2.63610.29661200.26262620X-RAY DIFFRACTION100
2.6361-2.72110.27181180.25772558X-RAY DIFFRACTION100
2.7211-2.81840.29641470.24542589X-RAY DIFFRACTION100
2.8184-2.93120.31761280.25042594X-RAY DIFFRACTION100
2.9312-3.06460.29891630.24792555X-RAY DIFFRACTION100
3.0646-3.22610.26891230.23792631X-RAY DIFFRACTION100
3.2261-3.42810.23911500.21572603X-RAY DIFFRACTION100
3.4281-3.69260.21311160.20372644X-RAY DIFFRACTION100
3.6926-4.06390.22431520.19222613X-RAY DIFFRACTION100
4.0639-4.65120.18771510.14462618X-RAY DIFFRACTION100
4.6512-5.85720.18691520.15442671X-RAY DIFFRACTION100
5.8572-40.43190.1951340.17622717X-RAY DIFFRACTION95

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