7ETW | pdb_00007etw

Cryo-EM structure of Scap/Insig complex in the present of digitonin.

PDB DOI: https://doi.org/10.2210/pdb7ETW/pdb
EM Map EMD-31303: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTM

Deposited: 2021-05-14 Released: 2021-06-23
Deposition Author(s): Yan, R., Cao, P., Song, W., Li, Y., Wang, T., Qian, H., Yan, C., Yan, N.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structural basis for sterol sensing by Scap and Insig

Yan, R., Cao, P., Song, W., Li, Y., Wang, T., Qian, H., Yan, C., Yan, N.

(2021) Cell Rep 35: 109299

DOI: https://doi.org/10.1016/j.celrep.2021.109299

Macromolecule Content

Total Structure Weight: 111.95 kDa
Atom Count: 4,952
Modeled Residue Count: 680
Deposited Residue Count: 960
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-induced gene 2 protein	A	225	Homo sapiens	Mutation(s): 3 Gene Names: INSIG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5U4 (Homo sapiens) Explore Q9Y5U4 Go to UniProtKB: Q9Y5U4
PHAROS: Q9Y5U4 GTEx: ENSG00000125629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5U4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sterol regulatory element-binding protein cleavage-activating protein	B	735	Homo sapiens	Mutation(s): 0 Gene Names: SCAP, KIAA0199, PSEC0227 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q12770 (Homo sapiens) Explore Q12770 Go to UniProtKB: Q12770
PHAROS: Q12770 GTEx: ENSG00000114650
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12770
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: Q12770-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth D]	2		N-Glycosylation	Interactions Focus chain C [auth D] Interactions & Density Focus chain C [auth D]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJP (Subject of Investigation/LOI) Query on AJP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	Digitonin C₅₆ H₉₂ O₂₉ UVYVLBIGDKGWPX-KUAJCENISA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2021-06-23
Type: Initial release
Version 2.0: 2021-09-22
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2022-03-02
Changes: Database references
Version 2.2: 2024-10-23
Changes: Data collection, Structure summary