9B62

Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model

PDB DOI: https://doi.org/10.2210/pdb9B62/pdb
EM Map EMD-44235: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-03-23 Released: 2024-10-16
Deposition Author(s): Lima, C.D., DiMattia, M.A.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure and activities of a human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex

Baytshtok, V., DiMattia, M.A., Lima, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 337.26 kDa
Atom Count: 19,287
Modelled Residue Count: 2,414
Deposited Residue Count: 2,990
Unique protein chains: 6

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1	A	1,074	Homo sapiens	Mutation(s): 0 Gene Names: XPO1, CRM1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens) Explore O14980 Go to UniProtKB: O14980
PHAROS: O14980 GTEx: ENSG00000082898
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14980
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	B, F	222	Homo sapiens	Mutation(s): 1 Gene Names: RAN, ARA24, OK/SW-cl.81 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens) Explore P62826 Go to UniProtKB: P62826
PHAROS: P62826 GTEx: ENSG00000132341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62826
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SUMO-conjugating enzyme UBC9	C	161	Homo sapiens	Mutation(s): 0 Gene Names: UBE2I, UBC9, UBCE9 EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63279 (Homo sapiens) Explore P63279 Go to UniProtKB: P63279
PHAROS: P63279 GTEx: ENSG00000103275
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63279
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ubiquitin-related modifier 1	D	101	Homo sapiens	Mutation(s): 1 Gene Names: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens) Explore P63165 Go to UniProtKB: P63165
PHAROS: P63165 GTEx: ENSG00000116030
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63165
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase RanBP2	E	619	Homo sapiens	Mutation(s): 0 Gene Names: RANBP2, NUP358 EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P49792 (Homo sapiens) Explore P49792 Go to UniProtKB: P49792
PHAROS: P49792 GTEx: ENSG00000153201
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49792
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran GTPase-activating protein 1	G	591	Homo sapiens	Mutation(s): 0 Gene Names: RANGAP1, KIAA1835, SD
UniProt & NIH Common Fund Data Resources
Find proteins for P46060 (Homo sapiens) Explore P46060 Go to UniProtKB: P46060
PHAROS: P46060 GTEx: ENSG00000100401
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46060
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth F] MOL2 format, chain H [auth B] MOL2 format, chain J [auth F] mmCIF format, chain H [auth B] mmCIF format, chain J [auth F]	H [auth B], J [auth F]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain H [auth B] Focus chain J [auth F] Interactions & Density Focus chain H [auth B] Focus chain J [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth F] MOL2 format, chain I [auth B] MOL2 format, chain K [auth F] mmCIF format, chain I [auth B] mmCIF format, chain K [auth F]	I [auth B], K [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth F] Interactions & Density Focus chain I [auth B] Focus chain K [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Lima, C.D.

DiMattia, M.A.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118080