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- PDB-5t4z: STRUCTURE OF THE ANTI-HIV ANTIBODY DH501 THAT BINDS GP120 V3 GLYC... -

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Basic information

Entry
Database: PDB / ID: 5t4z
TitleSTRUCTURE OF THE ANTI-HIV ANTIBODY DH501 THAT BINDS GP120 V3 GLYCAN AND THE BASE OF V3 WITH FREE MAN9 GLYCAN
Components
  • antibody DH501 Fab heavy chain
  • antibody DH501 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 antibody gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 Å
AuthorsNicely, N.I. / Haynes, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2017
Title: Vaccine Elicitation of High Mannose-Dependent Neutralizing Antibodies against the V3-Glycan Broadly Neutralizing Epitope in Nonhuman Primates.
Authors: Saunders, K.O. / Nicely, N.I. / Wiehe, K. / Bonsignori, M. / Meyerhoff, R.R. / Parks, R. / Walkowicz, W.E. / Aussedat, B. / Wu, N.R. / Cai, F. / Vohra, Y. / Park, P.K. / Eaton, A. / Go, E.P. ...Authors: Saunders, K.O. / Nicely, N.I. / Wiehe, K. / Bonsignori, M. / Meyerhoff, R.R. / Parks, R. / Walkowicz, W.E. / Aussedat, B. / Wu, N.R. / Cai, F. / Vohra, Y. / Park, P.K. / Eaton, A. / Go, E.P. / Sutherland, L.L. / Scearce, R.M. / Barouch, D.H. / Zhang, R. / Von Holle, T. / Overman, R.G. / Anasti, K. / Sanders, R.W. / Moody, M.A. / Kepler, T.B. / Korber, B. / Desaire, H. / Santra, S. / Letvin, N.L. / Nabel, G.J. / Montefiori, D.C. / Tomaras, G.D. / Liao, H.X. / Alam, S.M. / Danishefsky, S.J. / Haynes, B.F.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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 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: antibody DH501 Fab heavy chain
L: antibody DH501 Fab light chain
A: antibody DH501 Fab heavy chain
B: antibody DH501 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5837
Polymers94,9984
Non-polymers5853
Water6,359353
1
H: antibody DH501 Fab heavy chain
L: antibody DH501 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0845
Polymers47,4992
Non-polymers5853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-36 kcal/mol
Surface area20140 Å2
MethodPISA
2
A: antibody DH501 Fab heavy chain
B: antibody DH501 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4992
Polymers47,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-24 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.757, 115.997, 76.889
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody antibody DH501 Fab heavy chain


Mass: 24641.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody antibody DH501 Fab light chain


Mass: 22857.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M CaCl2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→34.49 Å / Num. obs: 58802 / % possible obs: 100 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIE

5iie


Resolution: 1.991→34.485 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.83
RfactorNum. reflection% reflection
Rfree0.2387 1997 3.4 %
Rwork0.1872 --
obs0.189 58683 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.991→34.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 36 354 6900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096713
X-RAY DIFFRACTIONf_angle_d1.1869164
X-RAY DIFFRACTIONf_dihedral_angle_d13.0872395
X-RAY DIFFRACTIONf_chiral_restr0.0491072
X-RAY DIFFRACTIONf_plane_restr0.0061160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.991-2.04080.31431330.23873790X-RAY DIFFRACTION94
2.0408-2.0960.37931420.30034034X-RAY DIFFRACTION99
2.096-2.15770.32921430.24664058X-RAY DIFFRACTION100
2.1577-2.22730.31011430.24994029X-RAY DIFFRACTION100
2.2273-2.30690.36021410.29973998X-RAY DIFFRACTION98
2.3069-2.39920.26231450.23254106X-RAY DIFFRACTION100
2.3992-2.50840.26811420.22364049X-RAY DIFFRACTION100
2.5084-2.64060.31091430.23184076X-RAY DIFFRACTION100
2.6406-2.8060.32561420.23334050X-RAY DIFFRACTION100
2.806-3.02250.27751450.22044091X-RAY DIFFRACTION100
3.0225-3.32650.27191440.20314099X-RAY DIFFRACTION100
3.3265-3.80730.23631440.17714066X-RAY DIFFRACTION100
3.8073-4.79470.16641440.12764093X-RAY DIFFRACTION100
4.7947-34.49050.15141460.12884147X-RAY DIFFRACTION100
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)
13.428-0.74340.03733.5652-1.19822.3936-0.0505-0.2593-0.05070.3616-0.1292-0.187-0.12910.17860.1620.2131-0.0265-0.01780.27660.05350.222963.115129.1068-3.4726
22.9264-2.2569-1.84353.39220.80513.94740.00080.2366-0.2863-0.27810.08080.40160.3961-0.3736-0.06180.2603-0.1282-0.06430.41190.11320.448278.50819.8157-29.1907
33.14520.1720.19844.70740.86682.31210.0310.0024-0.11350.60390.0013-0.53930.16420.4858-0.02780.33960.0097-0.09030.42570.0730.268574.566213.75255.3128
43.5362-0.121-0.46296.7031-2.59446.999-0.1606-0.0603-0.1854-0.18160.1913-0.47040.82630.031-0.00330.27440.0010.00090.2226-0.0430.307994.734517.1471-27.9041
50.74630.3883-0.47361.572-0.58442.9691-0.05560.202-0.0433-0.2152-0.01380.038-0.2291-0.27610.06340.23940.0374-0.02760.2572-0.03790.245446.024-12.454716.7295
61.7640.1252-0.37773.03181.91796.19830.0539-0.16220.11240.3145-0.22560.4126-0.1032-0.78460.16920.23780.030.03760.3329-0.01370.328131.5347-15.180650.5708
73.1236-0.1715-1.47934.16811.69294.68790.0387-0.15310.20850.13770.0447-0.1807-0.35640.1305-0.08240.25840.0054-0.04050.17710.0170.210757.34643.881823.8342
82.56520.32960.33256.2975-0.96115.3407-0.0991-0.0513-0.17260.06080.1717-0.93790.09880.3621-0.05990.2516-0.003-0.00330.2658-0.05380.414247.4308-14.675852.955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:107)
2X-RAY DIFFRACTION2(chain A and resid 108:212)
3X-RAY DIFFRACTION3(chain B and resid 3:107)
4X-RAY DIFFRACTION4(chain B and resid 108:208)
5X-RAY DIFFRACTION5(chain H and resid 1:126)
6X-RAY DIFFRACTION6(chain H and resid 130:218)
7X-RAY DIFFRACTION7(chain L and resid 3:107)
8X-RAY DIFFRACTION8(chain L and resid 108:211)

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