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- PDB-6p8n: Crystal Structure of Antibody P-p1f1 in Complex with eOD-GT8 -

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Basic information

Entry
Database: PDB / ID: 6p8n
TitleCrystal Structure of Antibody P-p1f1 in Complex with eOD-GT8
Components
  • Env outer domain eOD-GT8
  • P-p1f1 Heavy Chain
  • P-p1f1 Light Chain
KeywordsIMMUNE SYSTEM / antibody / immunization
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / AMMONIUM ION
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.202 Å
AuthorsWeidle, C. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109632 United States
CitationJournal: Cell Rep / Year: 2019
Title: Overcoming Steric Restrictions of VRC01 HIV-1 Neutralizing Antibodies through Immunization.
Authors: Parks, K.R. / MacCamy, A.J. / Trichka, J. / Gray, M. / Weidle, C. / Borst, A.J. / Khechaduri, A. / Takushi, B. / Agrawal, P. / Guenaga, J. / Wyatt, R.T. / Coler, R. / Seaman, M. / LaBranche, ...Authors: Parks, K.R. / MacCamy, A.J. / Trichka, J. / Gray, M. / Weidle, C. / Borst, A.J. / Khechaduri, A. / Takushi, B. / Agrawal, P. / Guenaga, J. / Wyatt, R.T. / Coler, R. / Seaman, M. / LaBranche, C. / Montefiori, D.C. / Veesler, D. / Pancera, M. / McGuire, A. / Stamatatos, L.
History
DepositionJun 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Env outer domain eOD-GT8
H: P-p1f1 Heavy Chain
L: P-p1f1 Light Chain
A: Env outer domain eOD-GT8
B: P-p1f1 Heavy Chain
D: P-p1f1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,02613
Polymers136,5646
Non-polymers4627
Water88349
1
C: Env outer domain eOD-GT8
H: P-p1f1 Heavy Chain
L: P-p1f1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7078
Polymers68,2823
Non-polymers4255
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Env outer domain eOD-GT8
B: P-p1f1 Heavy Chain
D: P-p1f1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3185
Polymers68,2823
Non-polymers362
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.879, 92.406, 223.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-302-

NH4

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Components

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Antibody , 2 types, 4 molecules HBLD

#2: Antibody P-p1f1 Heavy Chain


Mass: 24365.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#3: Antibody P-p1f1 Light Chain


Mass: 23738.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 3 molecules CA

#1: Protein Env outer domain eOD-GT8


Mass: 20178.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK 293s GNTI(-/-) / Production host: Homo sapiens (human)
#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 / N-Acetylglucosamine


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 , 3 types, 55 molecules

#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.56 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 22.5% PEG 3350, 13.5% Isopropanol, 0.18M Ammonium Citrate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2019
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: 20701 / % possible obs: 98.7 % / Redundancy: 6.2 % / CC1/2: 0.97 / Net I/σ(I): 7.89
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1703 / CC1/2: 0.659 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPK

4jpk


Resolution: 3.202→41.165 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.75
RfactorNum. reflection% reflection
Rfree0.2873 1023 4.96 %
Rwork0.2261 --
obs0.2291 20643 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.202→41.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8677 0 29 49 8755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038905
X-RAY DIFFRACTIONf_angle_d0.66512132
X-RAY DIFFRACTIONf_dihedral_angle_d7.0945623
X-RAY DIFFRACTIONf_chiral_restr0.0451354
X-RAY DIFFRACTIONf_plane_restr0.0041574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2024-3.37120.35371340.29242431X-RAY DIFFRACTION85
3.3712-3.58230.35941380.26622650X-RAY DIFFRACTION93
3.5823-3.85870.31431620.24282858X-RAY DIFFRACTION100
3.8587-4.24660.26871340.21442908X-RAY DIFFRACTION100
4.2466-4.86030.25991400.18582910X-RAY DIFFRACTION100
4.8603-6.12020.26181430.212869X-RAY DIFFRACTION97
6.1202-41.16830.2741720.23892994X-RAY DIFFRACTION97

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