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- PDB-6wit: Crystal structure of NHP D15.SD7 Fab in complex with 16055 V1V2 1... -

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Basic information

Entry
Database: PDB / ID: 6wit
TitleCrystal structure of NHP D15.SD7 Fab in complex with 16055 V1V2 1FD6 scaffold
Components
  • (NHP GN1-SD7 Fab ...) x 2
  • 16055 V1V2 1FD6 Scaffold
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / Fab / HIV / V1V2 / Complex / Antibody / Scaffold / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsLiban, T. / Aljedani, S. / Rodarte, J. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI104722 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization.
Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / ...Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / O'Dell, S. / Mascola, J.R. / Lee, K.K. / Karlsson Hedestam, G.B. / Wyatt, R.T. / Pancera, M.
History
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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

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Assembly

Deposited unit
A: NHP GN1-SD7 Fab Heavy Chain
B: NHP GN1-SD7 Fab Light Chain
C: 16055 V1V2 1FD6 Scaffold
H: NHP GN1-SD7 Fab Heavy Chain
L: NHP GN1-SD7 Fab Light Chain
I: 16055 V1V2 1FD6 Scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,06314
Polymers123,7946
Non-polymers1,2698
Water1,27971
1
A: NHP GN1-SD7 Fab Heavy Chain
B: NHP GN1-SD7 Fab Light Chain
C: 16055 V1V2 1FD6 Scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2145
Polymers61,8973
Non-polymers3172
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: NHP GN1-SD7 Fab Heavy Chain
L: NHP GN1-SD7 Fab Light Chain
I: 16055 V1V2 1FD6 Scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8499
Polymers61,8973
Non-polymers9526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.409, 89.809, 172.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody NHP GN1-SD7 Fab Heavy Chain


Mass: 25107.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): 293e / Production host: Homo sapiens (human)
#2: Antibody NHP GN1-SD7 Fab Light Chain


Mass: 22793.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): 293e / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 6 molecules CI

#3: Protein 16055 V1V2 1FD6 Scaffold


Mass: 13995.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293e / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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, 75 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 22% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 21, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→48.4813 Å / Num. obs: 28183 / % possible obs: 95.72 % / Redundancy: 6.2 % / Biso Wilson estimate: 49.64 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.049 / Rrim(I) all: 0.125 / Rsym value: 0.084 / Χ2: 0.936 / Net I/σ(I): 16.05
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 1436 / CC1/2: 0.573 / CC star: 0.853 / Rpim(I) all: 0.573 / Rrim(I) all: 0.495 / Rsym value: 0.408 / % possible all: 66.75

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RFO

4rfo


Resolution: 2.79→48.48 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 2000 7.1 %
Rwork0.2239 --
obs0.2282 28183 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8057 0 76 71 8204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058313
X-RAY DIFFRACTIONf_angle_d0.74711322
X-RAY DIFFRACTIONf_dihedral_angle_d18.32951
X-RAY DIFFRACTIONf_chiral_restr0.0491287
X-RAY DIFFRACTIONf_plane_restr0.0061450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.860.3505910.28081185X-RAY DIFFRACTION61
2.86-2.940.37251240.27651625X-RAY DIFFRACTION85
2.94-3.030.34591390.25891830X-RAY DIFFRACTION96
3.03-3.130.32381470.25671915X-RAY DIFFRACTION99
3.13-3.240.34551460.24981914X-RAY DIFFRACTION98
3.24-3.370.35171470.23431926X-RAY DIFFRACTION100
3.37-3.520.32681470.23151927X-RAY DIFFRACTION100
3.52-3.710.31361480.22271939X-RAY DIFFRACTION100
3.71-3.940.31041480.21551948X-RAY DIFFRACTION100
3.94-4.240.25691490.19391936X-RAY DIFFRACTION100
4.24-4.670.20291500.17131973X-RAY DIFFRACTION100
4.67-5.340.23141510.18661974X-RAY DIFFRACTION100
5.34-6.730.23671530.23922001X-RAY DIFFRACTION100
6.73-48.480.29681600.26142090X-RAY DIFFRACTION100

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