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- PDB-8tdx: TRNM-b.01 in complex with HIV Env fusion peptide -

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Basic information

Entry
Database: PDB / ID: 8tdx
TitleTRNM-b.01 in complex with HIV Env fusion peptide
Components
  • Env Fusion Peptide
  • TRNM-b.01 Fab Heavy Chain
  • TRNM-b.01 Fab Light Chain
KeywordsIMMUNE SYSTEM / HIV-1 / Fusion Peptide / Antibody / Fab
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsOlia, A.S. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques
Authors: Wang, H. / Olia, A.S. / Kwong, P.D.
History
DepositionJul 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRNM-b.01 Fab Heavy Chain
C: TRNM-b.01 Fab Light Chain
D: TRNM-b.01 Fab Light Chain
B: TRNM-b.01 Fab Heavy Chain
F: Env Fusion Peptide
E: Env Fusion Peptide


Theoretical massNumber of molelcules
Total (without water)97,2366
Polymers97,2366
Non-polymers00
Water13,655758
1
A: TRNM-b.01 Fab Heavy Chain
D: TRNM-b.01 Fab Light Chain
E: Env Fusion Peptide


Theoretical massNumber of molelcules
Total (without water)48,6183
Polymers48,6183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-24 kcal/mol
Surface area19740 Å2
MethodPISA
2
C: TRNM-b.01 Fab Light Chain
B: TRNM-b.01 Fab Heavy Chain
F: Env Fusion Peptide


Theoretical massNumber of molelcules
Total (without water)48,6183
Polymers48,6183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-22 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.464, 88.926, 129.108
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

#1: Antibody TRNM-b.01 Fab Heavy Chain


Mass: 24834.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody TRNM-b.01 Fab Light Chain


Mass: 23050.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide Env Fusion Peptide / Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P12489
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2M Sodium Chloride 21% PEG 8K 0.1M Sodium Phosphate / Citric Acid pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 57876 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.113 / Net I/σ(I): 14.48
Reflection shellResolution: 2.09→2.14 Å / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 2853 / CC1/2: 0.834 / CC star: 0.954

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→44.46 Å / SU ML: 0.1851 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 1997 3.49 %
Rwork0.2044 55292 -
obs0.2057 57289 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.08 Å2
Refinement stepCycle: LAST / Resolution: 2.09→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 0 758 7500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376892
X-RAY DIFFRACTIONf_angle_d0.73299384
X-RAY DIFFRACTIONf_chiral_restr0.0491084
X-RAY DIFFRACTIONf_plane_restr0.00491190
X-RAY DIFFRACTIONf_dihedral_angle_d6.0892946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.26791270.23543463X-RAY DIFFRACTION87.6
2.14-2.20.31751440.2383928X-RAY DIFFRACTION99.05
2.2-2.260.27131440.23943938X-RAY DIFFRACTION99.05
2.26-2.340.24681330.233922X-RAY DIFFRACTION98.85
2.34-2.420.2461420.2293902X-RAY DIFFRACTION98.59
2.42-2.520.28021370.23383952X-RAY DIFFRACTION99.27
2.52-2.630.25941500.23363959X-RAY DIFFRACTION99.35
2.63-2.770.29831430.23163986X-RAY DIFFRACTION99.54
2.77-2.950.27421480.22083965X-RAY DIFFRACTION99.54
2.95-3.170.29911420.21934000X-RAY DIFFRACTION99.45
3.17-3.490.23011400.20183993X-RAY DIFFRACTION98.8
3.49-40.20811500.18414018X-RAY DIFFRACTION99.55
4-5.030.17971450.15674086X-RAY DIFFRACTION99.72
5.04-44.460.21691520.1964180X-RAY DIFFRACTION98.01

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