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

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Basic information

Entry
Database: PDB / ID: 6uul
TitleCrystal structure of broad and potent HIV-1 neutralizing antibody 438-D5
Components
  • D5 Fab Heavy Chain
  • D5 Fab Light Chain
KeywordsIMMUNE SYSTEM / V3 glycan supersite / human antibody / ANTI-HIV NEUTRALIZING ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 30, 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
A: D5 Fab Heavy Chain
B: D5 Fab Light Chain
C: D5 Fab Heavy Chain
D: D5 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2337
Polymers97,3494
Non-polymers8843
Water7,314406
1
A: D5 Fab Heavy Chain
B: D5 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2453
Polymers48,6752
Non-polymers5711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-18 kcal/mol
Surface area21560 Å2
MethodPISA
2
C: D5 Fab Heavy Chain
D: D5 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9884
Polymers48,6752
Non-polymers3132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-21 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.731, 97.870, 125.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody D5 Fab Heavy Chain


Mass: 25263.596 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 D5 Fab Light Chain


Mass: 23410.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
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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Non-polymers , 2 types, 407 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.095M sodium citrate-citric acid (pH=6.2), 16%(v/v) 2-propanol, 5% (v/v) glycerol, 17%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 71245 / % possible obs: 99.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 41.88 Å2 / CC1/2: 0.88 / Rpim(I) all: 0.05 / Rsym value: 0.19 / Net I/σ(I): 22.8
Reflection shellResolution: 2.07→2.14 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 6892 / CC1/2: 0.56 / Rpim(I) all: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Coot1.16_3549model building
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WL2

5wl2


Resolution: 2.06→46.37 Å / SU ML: 0.3218 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 3586 5.04 %
Rwork0.2005 67547 -
obs0.2027 71133 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.58 Å2
Refinement stepCycle: LAST / Resolution: 2.06→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6705 0 6 406 7117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276865
X-RAY DIFFRACTIONf_angle_d0.59289335
X-RAY DIFFRACTIONf_chiral_restr0.04571063
X-RAY DIFFRACTIONf_plane_restr0.00431189
X-RAY DIFFRACTIONf_dihedral_angle_d11.77914093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.080.46471020.46832220X-RAY DIFFRACTION85.56
2.08-2.110.39651200.37432591X-RAY DIFFRACTION99.89
2.11-2.140.40851250.32892622X-RAY DIFFRACTION100
2.14-2.170.33821290.31232576X-RAY DIFFRACTION100
2.17-2.210.31491470.30662568X-RAY DIFFRACTION100
2.21-2.250.3491460.33182568X-RAY DIFFRACTION99.85
2.25-2.280.41931720.34372531X-RAY DIFFRACTION99.34
2.28-2.330.31991390.27982604X-RAY DIFFRACTION99.89
2.33-2.370.36211170.27522589X-RAY DIFFRACTION100
2.37-2.420.34831300.26272581X-RAY DIFFRACTION100
2.42-2.470.2911550.24562555X-RAY DIFFRACTION100
2.47-2.530.30741610.24572598X-RAY DIFFRACTION100
2.53-2.590.3271330.24292602X-RAY DIFFRACTION100
2.59-2.660.27591240.22822605X-RAY DIFFRACTION100
2.66-2.740.26891530.22112595X-RAY DIFFRACTION99.96
2.74-2.830.2771190.22432600X-RAY DIFFRACTION99.96
2.83-2.930.28061550.22522601X-RAY DIFFRACTION100
2.93-3.050.31011380.21392599X-RAY DIFFRACTION99.96
3.05-3.190.24681540.21982612X-RAY DIFFRACTION99.96
3.19-3.350.25551320.20192614X-RAY DIFFRACTION100
3.35-3.560.21691290.18422647X-RAY DIFFRACTION99.96
3.56-3.840.19931290.18142637X-RAY DIFFRACTION100
3.84-4.220.18981600.16422647X-RAY DIFFRACTION100
4.22-4.840.16841390.13592667X-RAY DIFFRACTION100
4.84-6.090.20341370.14872687X-RAY DIFFRACTION100
6.09-46.370.20731410.16652831X-RAY DIFFRACTION99.97

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