2QBY | pdb_00002qby

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)

PDB DOI: https://doi.org/10.2210/pdb2QBY/pdb
NAKB: 2QBY

Classification: REPLICATION/DNA
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-06-18 Released: 2007-09-11
Deposition Author(s): Cunningham Dueber, E.L., Corn, J.E., Bell, S.D., Berger, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.269 (Depositor), 0.262 (DCC)
R-Value Work:
0.226 (Depositor), 0.220 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex.

Dueber, E.L., Corn, J.E., Bell, S.D., Berger, J.M.

(2007) Science 317: 1210-1213

PubMed: 17761879 Search on PubMed
DOI: https://doi.org/10.1126/science.1143690
Primary Citation Related Structures:
2QBY

PubMed Abstract:
The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.

Organizational Affiliation

Miller Institute for Basic Research in Science, 2536 Channing Way 5190, University of California, Berkeley, CA 94720, USA.

Macromolecule Content

Total Structure Weight: 108.92 kDa
Atom Count: 7,309
Modeled Residue Count: 800
Deposited Residue Count: 836
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 6 homolog 1	C [auth A]	386	Saccharolobus solfataricus	Mutation(s): 0 Gene Names: cdc6-1
UniProt
Find proteins for Q980N4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q980N4 Go to UniProtKB: Q980N4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q980N4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 6 homolog 3	D [auth B]	384	Saccharolobus solfataricus	Mutation(s): 0 Gene Names: cdc6-3
UniProt
Find proteins for Q97WM8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97WM8 Go to UniProtKB: Q97WM8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97WM8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (33-MER)	A [auth C]	33	N/A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (33-MER)	B [auth D]	33	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A], K [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain I [auth A] Focus chain K [auth B]
SPD Query on SPD Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C]	E [auth C], F [auth C]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.269 (Depositor), 0.262 (DCC)
R-Value Work: 0.226 (Depositor), 0.220 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.649	α = 90
b = 199.143	β = 90
c = 213.405	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Cunningham Dueber, E.L.

Corn, J.E.

Bell, S.D.

Berger, J.M.

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description