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- PDB-4rbp: Crystal structure of HIV neutralizing antibody 2G12 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4rbp
TitleCrystal structure of HIV neutralizing antibody 2G12 in complex with a bacterial oligosaccharide analog of mammalian oligomanose
Components
  • Fab 2G12 heavy chain
  • Fab 2G12 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / HIV neutralizing / HIV-1 gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStanfield, R.L. / Wilson, I.A. / De Castro, C. / Marzaioli, A.M. / Pantophlet, R.
CitationJournal: Glycobiology / Year: 2015
Title: Crystal structure of the HIV neutralizing antibody 2G12 in complex with a bacterial oligosaccharide analog of mammalian oligomannose.
Authors: Stanfield, R.L. / De Castro, C. / Marzaioli, A.M. / Wilson, I.A. / Pantophlet, R.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

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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)96,93014
Polymers94,0954
Non-polymers2,83510
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-36 kcal/mol
Surface area39080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.300, 130.880, 170.100
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: 23201.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Fab 2G12 heavy chain


Mass: 23845.791 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-5)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid


Type: oligosaccharide / Mass: 1048.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]DManpa1-5DKdopa2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[Aad1122h-2a_2-6][a1122h-1a_1-5]/1-2-2-2-2-2/a5-b1_b3-c1_b6-f1_c2-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][a-D-Kdop]{[(5+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 33% PEG 600, 0.2M imidazole malate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.85→45.3 Å / Num. all: 77021 / Num. obs: 77021 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.576 / % possible all: 88

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OP5

1op5
PDB Unreleased entry


Resolution: 1.85→43.774 Å / SU ML: 0.21 / σ(F): 1 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 1999 2.6 %random
Rwork0.208 ---
obs0.2091 76919 87.94 %-
all-76919 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→43.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6586 0 190 495 7271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086974
X-RAY DIFFRACTIONf_angle_d1.2519482
X-RAY DIFFRACTIONf_dihedral_angle_d13.7472543
X-RAY DIFFRACTIONf_chiral_restr0.081111
X-RAY DIFFRACTIONf_plane_restr0.0051177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.33091250.26294679X-RAY DIFFRACTION78
1.8963-1.94760.33021260.24964742X-RAY DIFFRACTION80
1.9476-2.00490.31651300.23964846X-RAY DIFFRACTION81
2.0049-2.06960.27431310.2384886X-RAY DIFFRACTION81
2.0696-2.14360.32141310.24084915X-RAY DIFFRACTION82
2.1436-2.22940.32821340.24145026X-RAY DIFFRACTION84
2.2294-2.33080.27141390.24465181X-RAY DIFFRACTION86
2.3308-2.45370.27991430.25535366X-RAY DIFFRACTION89
2.4537-2.60740.29121470.25565555X-RAY DIFFRACTION92
2.6074-2.80870.31511530.23985678X-RAY DIFFRACTION93
2.8087-3.09130.29141520.2235745X-RAY DIFFRACTION94
3.0913-3.53840.24281570.19985890X-RAY DIFFRACTION96
3.5384-4.45740.18341620.15796041X-RAY DIFFRACTION98
4.4574-43.78650.19461690.16976370X-RAY DIFFRACTION99

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