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- PDB-5u1c: Structure of tetrameric HIV-1 Strand Transfer Complex Intasome -

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Basic information

Entry
Database: PDB / ID: 5u1c
TitleStructure of tetrameric HIV-1 Strand Transfer Complex Intasome
DescriptorDNA-binding protein 7d,Integrase/DNA Complex
KeywordsVIRAL PROTEIN / integrase / integration / transposase / transesterification
Specimen sourceSulfolobus solfataricus / archaea / thermophilic / スルホロブス・ソルファタリカス
Human immunodeficiency virus 1 / virus / HIV-1 / ヒト免疫不全ウイルス 1
Homo sapiens / human
MethodElectron microscopy (3.9 Å resolution / Particle / Single particle)
AuthorsLyumkis, D. / Passos, D.
CitationScience, 2017, 355, 89-92

Science, 2017, 355, 89-92 Yorodumi Papers
Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.
Dario Oliveira Passos / Min Li / Renbin Yang / Stephanie V Rebensburg / Rodolfo Ghirlando / Youngmin Jeon / Nikoloz Shkriabai / Mamuka Kvaratskhelia / Robert Craigie / Dmitry Lyumkis

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 28, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Jan 18, 2017Structure modelDatabase references / Source and taxonomy
1.2Sep 13, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: HIV-1 Integrase, Sso7d chimera
B: HIV-1 Integrase, Sso7d chimera
G: DNA (11-MER)
E: DNA (23-MER)
F: DNA (37-MER)
C: HIV-1 Integrase, Sso7d chimera
D: HIV-1 Integrase, Sso7d chimera
H: DNA (11-MER)
I: DNA (23-MER)
J: DNA (37-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,01914
Polyers212,83910
Non-polymers1794
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26400
ΔGint (kcal/M)-149
Surface area (Å2)49720

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Components

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Polypeptide(L) , 1 types, 4 molecules ABCD

#1: Polypeptide(L)
HIV-1 Integrase, Sso7d chimera / 7 kDa DNA-binding protein d / Sso7d


Mass: 42320.273 Da / Num. of mol.: 4 / Mutation: E152Q
Source: (gene. exp.) Sulfolobus solfataricus, (gene. exp.) Human immunodeficiency virus 1
References: UniProt: A0A157T5S7, UniProt: F2WR39

Cellular component

Molecular function

Biological process

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DNA chain , 3 types, 6 molecules GHEIFJ

#2: DNA chainDNA (11-MER)


Mass: 3349.197 Da / Num. of mol.: 2 / Source: (synth.) Homo sapiens
#3: DNA chainDNA (23-MER)


Mass: 7015.546 Da / Num. of mol.: 2 / Source: (synth.) Human immunodeficiency virus 1
#4: DNA chainDNA (37-MER)


Mass: 11414.358 Da / Num. of mol.: 2
Source: (synth.) Human immunodeficiency virus 1, (synth.) Homo sapiens

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Non-polymers , 2 types, 4 molecules

#5: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn
#6: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg

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Details

Sequence detailsThe protein is a chimera of Sso7d linked to the N-terminus of integrase via an 11-glycine linker.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer
Type: COMPLEX / Entity ID: 1,2,3,4 / Source: RECOMBINANT
Molecular weightValue: 0.228 deg. / Units: MEGADALTONS / Experimental value: YES
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Escherichia coli / Plasmid: pSca355
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1500mg/mLsodium chlorideNaCl1
220mMTrisC4H11NO31
30.5mMTCEPC9H15O6P1
46%glycerolC3H8O31
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 / Grid type: Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 50 % / Chamber temperature: 277 kelvins
Details: Sample containing HIV STC intasomes in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey gold UltrAuFoil grids (Quantifoil), adsorbed for 30 seconds, then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated magnification: 38167 / Calibrated defocus min: 1500 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 kelvins / Temperature (min): 90 kelvins
Image recordingAverage exposure time: 20 sec. / Electron dose: 95 e/Å2
Details: Individual frames were gain-corrected, aligned, and summed with the application of an exposure filter using MotionCor2, according to the nominal dose rate.
Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1225
Image scansSampling size: 5 microns / Dimension width: 3838 / Dimension height: 3710 / Movie frames/image: 100 / Used frames/image: 1-100

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Processing

SoftwareName: PHENIX / Version: dev_2499: / Classification: refinement
EM software
IDNameVersionCategoryImaging IDImage processing IDFitting IDDetails
2Leginon3.2IMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7Rosetta2015.12.57698_bundleMODEL FITTING1
8PHENIX2499MODEL FITTING1
9CootMODEL FITTING1
11RELION1.3INITIAL EULER ASSIGNMENT1
12FREALIGN9.11FINAL EULER ASSIGNMENT1
13FREALIGN3.11CLASSIFICATION1
14FREALIGN9.11RECONSTRUCTION1
15PHENIX2499MODEL REFINEMENT1real space refinement
16CootMODEL REFINEMENT1final details fixed and fitted manually
CTF correctionDetails: performed internally in Relion and Frealign / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 274764
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 83766 / Algorithm: FOURIER SPACE / Details: Resolution-limited refinement used throughout / Symmetry type: POINT
Atomic model buildingDetails: To generate ensemble models, the complete intasome model was iteratively relaxed - using two-fold symmetry and a combination of Rosetta and Phenix - against one half map (the working map) and inspected for consistency with the second half map (the free map). The model was then adjusted manually using Coot. Final ensemble modeling used half maps for all aspects of refinement and evaluation: 500 models were generated as described using Rosetta. From the 100 top-scoring models (scored by Rosetta energy), the ten models with the best map-to-model FSC were selected and refined in real space using secondary-structure restraints in Phenix. Molprobity was used throughout the refinement process.
Overall b value: 180 / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: FSC 0.5

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