+Open data
-Basic information
Entry | Database: PDB / ID: 6igm | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of Human SRCAP Complex | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / SRCAP complex | ||||||
Function / homology | Function and homology information promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body ...promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / nucleolus organization / box C/D snoRNP assembly / protein folding chaperone complex / ATP-dependent chromatin remodeler activity / negative regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of double-strand break repair via homologous recombination / positive regulation of transcription by RNA polymerase I / regulation of DNA replication / MLL1 complex / TFIID-class transcription factor complex binding / regulation of embryonic development / Telomere Extension By Telomerase / nucleosome binding / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / histone acetyltransferase activity / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of DNA repair / DNA helicase activity / TBP-class protein binding / telomere maintenance / helicase activity / cellular response to estradiol stimulus / ADP binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / chromatin DNA binding / beta-catenin binding / nuclear matrix / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / protein folding / HATs acetylate histones / ATPase binding / histone binding / spermatogenesis / regulation of apoptotic process / DNA helicase / DNA recombination / transcription coactivator activity / protein stabilization / nuclear body / cytoskeleton / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / cadherin binding / cell cycle / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / ATP hydrolysis activity / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Feng, Y. / Tian, Y. / Wu, Z. / Xu, Y. | ||||||
Citation | Journal: Cell Res / Year: 2018 Title: Cryo-EM structure of human SRCAP complex. Authors: Yangyang Feng / Yuan Tian / Zihan Wu / Yanhui Xu / | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6igm.cif.gz | 596.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6igm.ent.gz | 451.6 KB | Display | PDB format |
PDBx/mmJSON format | 6igm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/6igm ftp://data.pdbj.org/pub/pdb/validation_reports/ig/6igm | HTTPS FTP |
---|
-Related structure data
Related structure data | 9668MC 9669C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 50296.914 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A Production host: mammal environmental sample (environmental samples) References: UniProt: Q9Y265, DNA helicase #2: Protein | Mass: 51222.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 Production host: mammal environmental sample (environmental samples) References: UniProt: Q9Y230, DNA helicase #3: Protein | | Mass: 45857.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR6, CDA12 Production host: mammal environmental sample (environmental samples) References: UniProt: Q9GZN1 #4: Protein | | Mass: 343915.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SRCAP, KIAA0309 Production host: mammal environmental sample (environmental samples) References: UniProt: Q6ZRS2, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #5: Protein | | Mass: 5294.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: mammal environmental sample (environmental samples) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SRCAP complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: mammal environmental sample (environmental samples) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 1.5625 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
---|---|
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130318 / Symmetry type: POINT |