9NUP | pdb_00009nup

SsoPfMCM:DNA class 1c from DNA 1

PDB DOI: https://doi.org/10.2210/pdb9NUP/pdb
EM Map EMD-49814: EMDB EMDataResource

Classification: REPLICATION, HYDROLASE/DNA
Organism(s): Saccharolobus solfataricus P2, Pyrococcus furiosus DSM 3638, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-19 Released: 2026-03-25
Deposition Author(s): Enemark, E.J., Rasouli, S., Myasnikov, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

SsoPfMCM:DNA class 1c from DNA 1

Enemark, E.J., Rasouli, S., Myasnikov, A.

To be published.

Macromolecule Content

Total Structure Weight: 456.02 kDa
Atom Count: 27,137
Modeled Residue Count: 3,278
Deposited Residue Count: 3,798
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minichromosome maintenance protein MCM,DNA helicase	A, B, C, D, E A, B, C, D, E, F	613	Saccharolobus solfataricus P2, Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: MCM, SSO0774, PFDSM3638_02400 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for Q9UXG1 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q9UXG1 Go to UniProtKB: Q9UXG1
Find proteins for A0A5C0XP52 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore A0A5C0XP52 Go to UniProtKB: A0A5C0XP52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q9UXG1A0A5C0XP52
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (60-MER)	G [auth X], H [auth Y]	60	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth E] SDF format, chain T [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth F]	I [auth A], L [auth B], Q [auth E], T [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth E] Focus chain T [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] SDF format, chain O [auth C] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] MOL2 format, chain O [auth C] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F] mmCIF format, chain O [auth C]	K [auth A] N [auth B] O [auth C] P [auth D] S [auth E] K [auth A], N [auth B], O [auth C], P [auth D], S [auth E], V [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain R [auth E] SDF format, chain U [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F]	J [auth A], M [auth B], R [auth E], U [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth E] Focus chain U [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth E] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Enemark, E.J.

Rasouli, S.

Myasnikov, A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM136313
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20 GM152281
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20 GM103429