[English] 日本語
- PDB-5u1c: Structure of tetrameric HIV-1 Strand Transfer Complex Intasome -

Open data

ID or keywords:


no data

Basic information

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 A resolution / Single particle)
AuthorsLyumkis, D. / Passos, D.
CitationScience, 2017, 355, 89-92

Science, 2017, 355, 89-92 StrPapers
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

DateDeposition: Nov 28, 2016 / Release: Jan 11, 2017 / Last modification: Jan 18, 2017

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /

Downloads & links


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

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)26400
ΔGint (kcal/M)-149
Surface area (A2)49720


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

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

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


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

Experimental details


EM experimentReconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer
Specimen supportGrid material: GOLD / Grid mesh size: 400 / Grid type: Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 50 %
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.

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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated magnification: 38167 / Cs: 2.7
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 / Temperature (min): 90
EM image scansSampling size: 5


SoftwareName: PHENIX / Version: dev_2499: / Classification: refinement
ComputingStructure refinement: PHENIX (dev_2499: phenix.real_space_refine)
3D reconstructionResolution: 3.9 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 83766 / Details: Resolution-limited refinement used throughout
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

About Yorodumi


Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more