5V8F | pdb_00005v8f

Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1

PDB DOI: https://doi.org/10.2210/pdb5V8F/pdb
Entry: 5V8F supersedes: 5UDB
NAKB: 5V8F
EM Map EMD-8540: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2017-03-21 Released: 2017-05-10
Deposition Author(s): Yuan, Z., Riera, A., Bai, L., Sun, J., Spanos, C., Chen, Z.A., Barbon, M., Rappsilber, J., Stillman, B., Speck, C., Li, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1.

Yuan, Z., Riera, A., Bai, L., Sun, J., Nandi, S., Spanos, C., Chen, Z.A., Barbon, M., Rappsilber, J., Stillman, B., Speck, C., Li, H.

(2017) Nat Struct Mol Biol 24: 316-324

PubMed: 28191893 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.3372
Primary Citation Related Structures:
5V8F

PubMed Abstract:
To initiate DNA replication, the origin recognition complex (ORC) and Cdc6 load an Mcm2-7 double hexamer onto DNA. Without ATP hydrolysis, ORC-Cdc6 recruits one Cdt1-bound Mcm2-7 hexamer, thus forming an ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) helicase-loading intermediate. Here we report a 3.9-Å structure of Saccharomyces cerevisiae OCCM on DNA. Flexible Mcm2-7 winged-helix domains (WHDs) engage ORC-Cdc6. A three-domain Cdt1 configuration embraces Mcm2, Mcm4, and Mcm6, thus comprising nearly half of the hexamer. The Cdt1 C-terminal domain extends to the Mcm6 WHD, which binds the Orc4 WHD. DNA passes through the ORC-Cdc6 and Mcm2-7 rings. Origin DNA interaction is mediated by an α-helix within Orc4 and positively charged loops within Orc2 and Cdc6. The Mcm2-7 C-tier AAA+ ring is topologically closed by an Mcm5 loop that embraces Mcm2, but the N-tier-ring Mcm2-Mcm5 interface remains open. This structure suggests a loading mechanism of the first Cdt1-bound Mcm2-7 hexamer by ORC-Cdc6.

Organizational Affiliation

Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA.

Macromolecule Content

Total Structure Weight: 1,170.84 kDa
Atom Count: 59,586
Modeled Residue Count: 7,297
Deposited Residue Count: 10,151
Unique protein chains: 14
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2	A [auth 2]	868	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MCM2, YBL023C, YBL0438 EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29469 Go to UniProtKB: P29469
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29469
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM3	B [auth 3]	971	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MCM3, YEL032W, SYGP-ORF23 EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P24279 Go to UniProtKB: P24279
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24279
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM4	C [auth 4]	933	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MCM4, CDC54, HCD21, YPR019W, YP9531.13 EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30665 Go to UniProtKB: P30665
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30665
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Minichromosome maintenance protein 5	D [auth 5]	775	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MCM5, CDC46, YLR274W, L9328.1 EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29496 Go to UniProtKB: P29496
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29496
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM6	E [auth 6]	1,017	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MCM6, YGL201C EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53091 Go to UniProtKB: P53091
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53091
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	F [auth 7]	800	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MCM7, CDC47, YBR202W, YBR1441 EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38132 Go to UniProtKB: P38132
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UniProt Group	P38132
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division cycle protein CDT1	G [auth 8]	604	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: TAH11, CDT1, SID2, YJR046W, J1641
UniProt
Find proteins for P47112 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47112 Go to UniProtKB: P47112
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UniProt Group	P47112
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 6	H [auth 9]	513	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CDC6, YJL194W, J0347
UniProt
Find proteins for P09119 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09119 Go to UniProtKB: P09119
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UniProt Group	P09119
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 1	I [auth A]	913	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ORC1, YML065W
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P54784 Go to UniProtKB: P54784
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54784
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 2	J [auth B]	620	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ORC2, RRR1, SIR5, YBR060C, YBR0523
UniProt
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32833 Go to UniProtKB: P32833
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32833
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 3	K [auth C]	616	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ORC3, OAF1, OIF1, YLL004W, L1365
UniProt
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P54790 Go to UniProtKB: P54790
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54790
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 5	L [auth E]	479	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ORC5, YNL261W, N0834
UniProt
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P50874 Go to UniProtKB: P50874
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UniProt Group	P50874
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 4	M [auth D]	529	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ORC4, YPR162C, P9325.5
UniProt
Find proteins for P54791 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P54791 Go to UniProtKB: P54791
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UniProt Group	P54791
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 6	N [auth F]	435	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ORC6, AAP1, YHR118C
UniProt
Find proteins for P38826 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38826 Go to UniProtKB: P38826
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38826
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA (39-MER)	O [auth M]	39	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 16
DNA (39-MER)	P [auth N]	39	synthetic construct
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth E] SDF format, chain V [auth A] SDF format, chain U [auth 9] SDF format, chain T [auth 7] SDF format, chain S [auth 6] SDF format, chain R [auth 4] SDF format, chain Q [auth 2] MOL2 format, chain X [auth D] MOL2 format, chain W [auth E] MOL2 format, chain V [auth A] MOL2 format, chain U [auth 9] MOL2 format, chain T [auth 7] MOL2 format, chain S [auth 6] MOL2 format, chain R [auth 4] MOL2 format, chain Q [auth 2] mmCIF format, chain X [auth D] mmCIF format, chain W [auth E] mmCIF format, chain V [auth A] mmCIF format, chain U [auth 9] mmCIF format, chain T [auth 7] mmCIF format, chain S [auth 6] mmCIF format, chain R [auth 4] mmCIF format, chain Q [auth 2]	Q [auth 2] R [auth 4] S [auth 6] T [auth 7] U [auth 9] Q [auth 2], R [auth 4], S [auth 6], T [auth 7], U [auth 9], V [auth A], W [auth E], X [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain Q [auth 2] Focus chain R [auth 4] Focus chain S [auth 6] Focus chain T [auth 7] Focus chain U [auth 9] Focus chain V [auth A] Focus chain W [auth E] Focus chain X [auth D] Interactions & Density Focus chain Q [auth 2] Focus chain R [auth 4] Focus chain S [auth 6] Focus chain T [auth 7] Focus chain U [auth 9] Focus chain V [auth A] Focus chain W [auth E] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

This entry supersedes: 5UDB

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111742
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM45436
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	P56061
Wellcome Trust	United Kingdom	P56628

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Data collection
Version 1.2: 2017-11-08
Changes: Derived calculations, Experimental preparation
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 2.0: 2020-04-22
Type: Coordinate replacement
Reason: Chirality error
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2024-10-09
Changes: Data collection, Database references, Structure summary

5V8F | pdb_00005v8f

Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1

Literature

Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

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Entity ID: 11

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Entity ID: 13

UniProt

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Entity ID: 14

UniProt

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Entity ID: 15

Sequence Annotations

Entity ID: 16

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)