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- PDB-6vsl: Crystal structure of a human fucosylated IgG1 Fc expressed in tob... -

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Basic information

Entry
Database: PDB / ID: 6vsl
TitleCrystal structure of a human fucosylated IgG1 Fc expressed in tobacco plants (Nicotiana benthamiana)
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / immunoglobulin / crystallizable fragment / IgG1 / Fc
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI16274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: J.Virol. / Year: 2021
Title: Enhanced Ability of Plant-Derived PGT121 Glycovariants To Eliminate HIV-1-Infected Cells.
Authors: Anand, S.P. / Ding, S. / Tolbert, W.D. / Prevost, J. / Richard, J. / Gil, H.M. / Gendron-Lepage, G. / Cheung, W.F. / Wang, H. / Pastora, R. / Saxena, H. / Wakarchuk, W. / Medjahed, H. / ...Authors: Anand, S.P. / Ding, S. / Tolbert, W.D. / Prevost, J. / Richard, J. / Gil, H.M. / Gendron-Lepage, G. / Cheung, W.F. / Wang, H. / Pastora, R. / Saxena, H. / Wakarchuk, W. / Medjahed, H. / Wines, B.D. / Hogarth, M. / Shaw, G.M. / Martin, M.A. / Burton, D.R. / Hangartner, L. / Evans, D.T. / Pazgier, M. / Cossar, D. / McLean, M.D. / Finzi, A.
History
DepositionFeb 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct.title
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 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: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3236
Polymers47,8362
Non-polymers3,4874
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint51 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.860, 79.920, 138.540
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 Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 23918.043 Da / Num. of mol.: 2 / Fragment: crystallizable fragment (UNP residues 236-446)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Nicotiana benthamiana (plant) / References: UniProt: P0DOX5
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 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)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% PEG4000, 0.1 M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 26, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32561 / % possible obs: 98.7 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rpim(I) all: 0.061 / Rsym value: 0.097 / Net I/σ(I): 5.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4712 / CC1/2: 0.5 / Rpim(I) all: 0.479 / Rsym value: 0.775 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3AVE

3ave


Resolution: 2.1→46.91 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 26.67
RfactorNum. reflection% reflection
Rfree0.2499 2893 4.95 %
Rwork0.2075 --
obs0.2096 58447 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 236 189 3765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013687
X-RAY DIFFRACTIONf_angle_d1.1025026
X-RAY DIFFRACTIONf_dihedral_angle_d8.392601
X-RAY DIFFRACTIONf_chiral_restr0.06610
X-RAY DIFFRACTIONf_plane_restr0.007615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.37411270.33352663X-RAY DIFFRACTION94
2.13-2.170.38361520.32642666X-RAY DIFFRACTION95
2.17-2.210.39391380.32822643X-RAY DIFFRACTION95
2.21-2.250.32521540.31182694X-RAY DIFFRACTION95
2.25-2.30.28521230.30212691X-RAY DIFFRACTION94
2.3-2.350.35341270.29272680X-RAY DIFFRACTION95
2.35-2.40.28841400.26842674X-RAY DIFFRACTION94
2.4-2.460.3391590.26932624X-RAY DIFFRACTION94
2.46-2.530.26941440.26262635X-RAY DIFFRACTION94
2.53-2.610.33621350.25872610X-RAY DIFFRACTION92
2.61-2.690.28771430.23622551X-RAY DIFFRACTION91
2.69-2.790.29461340.23192592X-RAY DIFFRACTION90
2.79-2.90.27641200.22662622X-RAY DIFFRACTION94
2.9-3.030.31361240.22752602X-RAY DIFFRACTION92
3.03-3.190.24721480.21412653X-RAY DIFFRACTION94
3.19-3.390.23491440.19742691X-RAY DIFFRACTION96
3.39-3.650.22371510.19072755X-RAY DIFFRACTION96
3.65-4.020.25851480.18422653X-RAY DIFFRACTION96
4.02-4.60.18441210.15562697X-RAY DIFFRACTION95
4.6-5.790.19721210.15352555X-RAY DIFFRACTION90
5.79-46.910.18391400.16652603X-RAY DIFFRACTION92
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)
13.49470.92311.13362.02450.66162.7466-0.24010.24130.3117-0.04080.21980.0229-0.2288-0.03340.01510.19670.01110.03660.18910.02720.339310.207910.319342.7735
23.38190.1389-0.31114.99180.59242.779-0.2772-0.1443-0.43271.15190.2619-0.11530.53660.24880.01540.52540.0953-0.05390.2352-0.01560.3759-7.198-9.790845.1703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 235 through 444)
2X-RAY DIFFRACTION2(chain 'B' and resid 237 through 444)

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