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- PDB-6uuh: Crystal structure of broad and potent HIV-1 neutralizing antibody... -

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Basic information

Entry
Database: PDB / ID: 6uuh
TitleCrystal structure of broad and potent HIV-1 neutralizing antibody 438-B11
Components
  • B11 Fab Heavy Chain
  • B11 Fab Light Chain
  • Immunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / V3 glycan supersite / human antibody / ANTI-HIV NEUTRALIZING ANTIBODY / VIRAL PROTEIN
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus sp. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKumar, S. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2020
Title: A V H 1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite.
Authors: Kumar, S. / Ju, B. / Shapero, B. / Lin, X. / Ren, L. / Zhang, L. / Li, D. / Zhou, Z. / Feng, Y. / Sou, C. / Mann, C.J. / Hao, Y. / Sarkar, A. / Hou, J. / Nunnally, C. / Hong, K. / Wang, S. / ...Authors: Kumar, S. / Ju, B. / Shapero, B. / Lin, X. / Ren, L. / Zhang, L. / Li, D. / Zhou, Z. / Feng, Y. / Sou, C. / Mann, C.J. / Hao, Y. / Sarkar, A. / Hou, J. / Nunnally, C. / Hong, K. / Wang, S. / Ge, X. / Su, B. / Landais, E. / Sok, D. / Zwick, M.B. / He, L. / Zhu, J. / Wilson, I.A. / Shao, Y.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: B11 Fab Heavy Chain
D: B11 Fab Light Chain
E: Immunoglobulin G-binding protein G
A: B11 Fab Heavy Chain
B: B11 Fab Light Chain
F: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8138
Polymers112,1696
Non-polymers1,6442
Water00
1
C: B11 Fab Heavy Chain
D: B11 Fab Light Chain
E: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3064
Polymers56,0853
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: B11 Fab Heavy Chain
B: B11 Fab Light Chain
F: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5074
Polymers56,0853
Non-polymers1,4221
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.157, 72.751, 108.716
Angle α, β, γ (deg.)90.000, 101.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody B11 Fab Heavy Chain


Mass: 25291.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody B11 Fab Light Chain


Mass: 23444.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 7348.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: spg / Production host: Homo sapiens (human) / References: UniProt: P19909
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.085M sodium acetate (pH=4.0), 0.17M ammonium acetate, 5% %(v/v) glycerol, 27.882 %(w/v) PEG4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 29107 / % possible obs: 96.6 % / Redundancy: 3 % / Biso Wilson estimate: 57.4 Å2 / CC1/2: 0.89 / Rpim(I) all: 0.05 / Rsym value: 0.1 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 1479 / CC1/2: 0.54 / Rpim(I) all: 0.53 / Rsym value: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TFS

5tfs


Resolution: 2.7→48.22 Å / SU ML: 0.4221 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5564
RfactorNum. reflection% reflection
Rfree0.2602 1455 5 %
Rwork0.2273 --
obs0.229 29094 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.13 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7714 0 36 0 7750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317924
X-RAY DIFFRACTIONf_angle_d0.6710782
X-RAY DIFFRACTIONf_chiral_restr0.04591244
X-RAY DIFFRACTIONf_plane_restr0.00461364
X-RAY DIFFRACTIONf_dihedral_angle_d17.04362885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.3531440.32442730X-RAY DIFFRACTION95.39
2.8-2.910.36241460.30772794X-RAY DIFFRACTION97.93
2.91-3.040.36161460.31172760X-RAY DIFFRACTION97.62
3.04-3.20.34811430.29372711X-RAY DIFFRACTION94.94
3.2-3.40.31851450.2652756X-RAY DIFFRACTION96.35
3.4-3.660.28821470.24212795X-RAY DIFFRACTION98.63
3.66-4.030.24161480.2322813X-RAY DIFFRACTION97.85
4.03-4.620.20481450.19262740X-RAY DIFFRACTION95.53
4.62-5.810.22911430.18382721X-RAY DIFFRACTION94.62
5.81-48.220.22111480.18872819X-RAY DIFFRACTION95.1
Refinement TLS params.Method: refined / Origin x: -13.1160172483 Å / Origin y: 17.0409875715 Å / Origin z: -24.4600209547 Å
111213212223313233
T0.317033739765 Å20.101403056803 Å20.0097991480235 Å2-0.230170895428 Å2-0.143528830887 Å2--0.215373988371 Å2
L1.13001971031 °2-0.038882383011 °20.0714386346873 °2-0.0693617617471 °2-0.145141996743 °2--0.167262574524 °2
S-0.0983476505575 Å °0.0581723606584 Å °-0.128430784541 Å °0.0126632247346 Å °0.104040914344 Å °-0.0520121171933 Å °-0.0522109682686 Å °-0.0177052078631 Å °1.57180102562E-13 Å °
Refinement TLS groupSelection details: all

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