[English] 日本語
Yorodumi
- PDB-9van: Cryo-EM structure of human full length KICSTOR complex (state 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9van
TitleCryo-EM structure of human full length KICSTOR complex (state 2)
Components
  • KICSTOR complex protein ITFG2
  • KICSTOR complex protein SZT2
  • KICSTOR complex protein kaptin
  • KICSTOR subunit 2
KeywordsSIGNALING PROTEIN / Lipid binding protein
Function / homology
Function and homology information


regulation of superoxide dismutase activity / KICSTOR complex / corpus callosum morphogenesis / germinal center B cell differentiation / protein localization to lysosome / regulation of TOR signaling / Amino acids regulate mTORC1 / postsynaptic actin cytoskeleton / stereocilium / pigmentation ...regulation of superoxide dismutase activity / KICSTOR complex / corpus callosum morphogenesis / germinal center B cell differentiation / protein localization to lysosome / regulation of TOR signaling / Amino acids regulate mTORC1 / postsynaptic actin cytoskeleton / stereocilium / pigmentation / cellular response to glucose starvation / intercellular bridge / negative regulation of TORC1 signaling / cellular response to amino acid starvation / actin filament organization / central nervous system development / post-embryonic development / actin filament binding / peroxisome / lamellipodium / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
KICSTOR subunit 2 / KICSTOR complex protein C12orf66-like, central domain superfamily / KICSTOR complex C12orf66 like / Kaptin / Integrin-alpha FG-GAP repeat-containing protein 2 / Integrin-alpha FG-GAP repeat-containing protein 2 / Protein SZT2 / Integrin alpha, N-terminal / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
KICSTOR complex protein SZT2 / KICSTOR complex protein ITFG2 / KICSTOR subunit 2 / KICSTOR complex protein kaptin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSu, M.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government20231120103446003 China
CitationJournal: To Be Published
Title: Structure of KICSTOR complex
Authors: Su, M.-Y.
History
DepositionJun 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KICSTOR complex protein SZT2
B: KICSTOR complex protein ITFG2
C: KICSTOR complex protein kaptin
D: KICSTOR subunit 2


Theoretical massNumber of molelcules
Total (without water)526,4174
Polymers526,4174
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein KICSTOR complex protein SZT2 / Seizure threshold 2 protein homolog


Mass: 378453.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SZT2, C1orf84, KIAA0467 / Production host: Homo sapiens (human) / References: UniProt: Q5T011
#2: Protein KICSTOR complex protein ITFG2 / Integrin-alpha FG-GAP repeat-containing protein 2


Mass: 49365.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITFG2 / Production host: Homo sapiens (human) / References: UniProt: Q969R8
#3: Protein KICSTOR complex protein kaptin / Actin-associated protein 2E4


Mass: 48128.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPTN / Production host: Homo sapiens (human) / References: UniProt: Q9Y664
#4: Protein KICSTOR subunit 2 / KICSTOR complex protein C12orf66


Mass: 50469.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KICS2, C12orf66 / Production host: Homo sapiens (human) / References: UniProt: Q96MD2
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Structure of KICSTOR complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.525 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: SPOT SCAN / Model: TFS KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Specimen-ID: 1

ID
1
2
3
4
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1154.74GATAN K3 (6k x 4k)
2253.88GATAN K3 (6k x 4k)
3352.4GATAN K3 (6k x 4k)
4459.61GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
Image processing
IDImage recording-ID
11
22
33
44
CTF correction
IDEM image processing-IDType
11NONE
22NONE
33NONE
44NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280444 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514775
ELECTRON MICROSCOPYf_angle_d0.60220290
ELECTRON MICROSCOPYf_dihedral_angle_d4.0522286
ELECTRON MICROSCOPYf_chiral_restr0.0422477
ELECTRON MICROSCOPYf_plane_restr0.0052708

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more