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- PDB-5t33: Crystal structure of strain-specific glycan-dependent CD4 binding... -

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Basic information

Entry
Database: PDB / ID: 5t33
TitleCrystal structure of strain-specific glycan-dependent CD4 binding site-directed neutralizing antibody CAP257-RH1, in complex with HIV-1 strain RHPA gp120 core with an oligomannose N276 glycan.
Components
  • CAP257-RH1 heavy chain
  • CAP257-RH1 light chain
  • RHPA gp120 core
KeywordsIMMUNE SYSTEM / HIV / strain-specific / neutralizing antibody / CD4 binding site / N276 glycan / glycan-free V5
Function / homologyHIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2092 Å
AuthorsWibmer, C.K. / Gorman, J. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2016
Title: Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site.
Authors: Wibmer, C.K. / Gorman, J. / Anthony, C.S. / Mkhize, N.N. / Druz, A. / York, T. / Schmidt, S.D. / Labuschagne, P. / Louder, M.K. / Bailer, R.T. / Abdool Karim, S.S. / Mascola, J.R. / ...Authors: Wibmer, C.K. / Gorman, J. / Anthony, C.S. / Mkhize, N.N. / Druz, A. / York, T. / Schmidt, S.D. / Labuschagne, P. / Louder, M.K. / Bailer, R.T. / Abdool Karim, S.S. / Mascola, J.R. / Williamson, C. / Moore, P.L. / Kwong, P.D. / Morris, L.
History
DepositionAug 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Source and taxonomy
Revision 1.2Sep 28, 2016Group: Other
Revision 1.3Nov 16, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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_oper_list / struct_asym / struct_conn / struct_ref_seq / 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 / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_end
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 2.2Oct 30, 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: CAP257-RH1 heavy chain
L: CAP257-RH1 light chain
G: RHPA gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,00313
Polymers86,8433
Non-polymers4,16010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint43 kcal/mol
Surface area36120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.176, 71.139, 190.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules G

#3: Protein RHPA gp120 core


Mass: 39997.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human)

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Antibody , 2 types, 2 molecules HL

#1: Antibody CAP257-RH1 heavy chain


Mass: 23888.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Donor CAP257 / Source: (gene. exp.) Homo sapiens (human) / Tissue: Peripheral Blood Mononuclear Cells / Cell: Memory B cell / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody CAP257-RH1 light chain


Mass: 22957.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Donor CAP257 / Source: (gene. exp.) Homo sapiens (human) / Tissue: Peripheral Blood Mononuclear cells / Cell: Memory B cell / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Sugars , 4 types, 10 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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.: 6
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

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Details

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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH7.5) 8% PEG4000 10% Isopropanol 200U/mL Endo H 25% 2-Methyl-2,4-pentanediol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 13003 / % possible obs: 81.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 90.23 Å2 / Rmerge(I) obs: 0.102 / Net I/av σ(I): 10.724 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.2-3.272.30.3810.766133.1
3.27-3.362.70.3660.841154.4
3.36-3.452.80.3290.881171.7
3.45-3.553.20.3150.898179.2
3.55-3.663.50.2760.923184.6
3.66-3.793.70.2350.941185.6
3.79-3.953.70.2140.946184.7
3.95-4.133.80.1730.962185.9
4.13-4.343.70.1490.967186.5
4.34-4.613.70.1240.981186
4.61-4.973.70.1050.983188.6
4.97-5.473.60.0930.989191.6
5.47-6.263.60.0930.988197.8
6.26-7.883.70.0730.993198.4
7.88-503.50.0590.994196.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZZ, 4HPY, 1NL0

4jzz

4hpy

1nl0


Resolution: 3.2092→47.658 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.89
RfactorNum. reflection% reflection
Rfree0.2689 646 4.98 %
Rwork0.2287 --
obs0.2308 12967 81.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 249.5 Å2 / Biso mean: 116.9047 Å2 / Biso min: 55.53 Å2
Refinement stepCycle: final / Resolution: 3.2092→47.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5801 0 533 0 6334
Biso mean--153.96 --
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026245
X-RAY DIFFRACTIONf_angle_d0.5638537
X-RAY DIFFRACTIONf_chiral_restr0.0411015
X-RAY DIFFRACTIONf_plane_restr0.0031055
X-RAY DIFFRACTIONf_dihedral_angle_d8.2483566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2092-3.45690.3243850.2881586167154
3.4569-3.80470.31251210.26222455257683
3.8047-4.35490.25591360.22852535267186
4.3549-5.48550.21581390.21082678281788
5.4855-47.66350.29081650.22243067323298
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)
13.17770.1782-0.26385.6557-1.50425.7936-0.0809-0.16770.43380.11230.056-0.0547-0.20520.0651-0.02380.3740.0696-0.04110.4331-0.0240.80810.532915.1393-30.589
28.483-2.4256-1.928.78910.08498.10180.13540.422-0.005-0.0663-0.06840.44990.550.0594-0.03110.4001-0.0893-0.03140.47730.08890.559133.70718.461-52.2593
33.3287-0.2751-2.54794.31250.64077.6789-0.2379-0.205-0.6520.12470.2809-0.05940.27390.23780.06910.35060.0008-0.01520.41570.02041.10496.4425-5.3534-37.3871
45.17432.882.42978.70352.05647.43730.1311-0.0557-0.21840.0645-0.2816-0.3317-0.2849-0.00120.23420.40150.04570.14390.31550.00040.700431.01916.9027-41.7581
54.37140.92760.99782.1146-1.19612.0022-0.2185-0.8533-0.13850.4426-0.1509-0.0096-0.1169-0.40440.35450.656-0.02060.01850.803-0.00970.5572-22.67111.6662-4.2699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 120 )H1 - 120
2X-RAY DIFFRACTION2chain 'H' and (resid 121 through 222 )H121 - 222
3X-RAY DIFFRACTION3chain 'L' and (resid 2 through 108 )L2 - 108
4X-RAY DIFFRACTION4chain 'L' and (resid 109 through 213 )L109 - 213
5X-RAY DIFFRACTION5chain 'G' and (resid 45 through 492 )G45 - 492

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