4BXO | pdb_00004bxo

Architecture and DNA recognition elements of the Fanconi anemia FANCM- FAAP24 complex

PDB DOI: https://doi.org/10.2210/pdb4BXO/pdb
NAKB: 4BXO

Classification: HYDROLASE/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-15 Released: 2013-08-28
Deposition Author(s): Coulthard, R., Deans, A., Swuec, P., Bowles, M., Purkiss, A., Costa, A., West, S., McDonald, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.255 (Depositor), 0.281 (DCC)
R-Value Work:
0.204 (Depositor), 0.223 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Architecture and DNA Recognition Elements of the Fanconi Anemia Fancm-Faap24 Complex.

Coulthard, R., Deans, A.J., Swuec, P., Bowles, M., Costa, A., West, S.C., Mcdonald, N.Q.

(2013) Structure 21: 1648

PubMed: 23932590 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2013.07.006
Primary Citation Related Structures:
4BXO

PubMed Abstract:
Fanconi anemia (FA) is a disorder associated with a failure in DNA repair. FANCM (defective in FA complementation group M) and its partner FAAP24 target other FA proteins to sites of DNA damage. FANCM-FAAP24 is related to XPF/MUS81 endonucleases but lacks endonucleolytic activity. We report a structure of an FANCM C-terminal fragment (FANCMCTD) bound to FAAP24 and DNA. This S-shaped structure reveals the FANCM (HhH)2 domain is buried, whereas the FAAP24 (HhH)2 domain engages DNA. We identify a second DNA contact and a metal center within the FANCM pseudo-nuclease domain and demonstrate that mutations in either region impair double-stranded DNA binding in vitro and FANCM-FAAP24 function in vivo. We show the FANCM translocase domain lies in proximity to FANCMCTD by electron microscopy and that binding fork DNA structures stimulate its ATPase activity. This suggests a tracking model for FANCM-FAAP24 until an encounter with a stalled replication fork triggers ATPase-mediated fork remodeling.

Organizational Affiliation

Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.

Macromolecule Content

Total Structure Weight: 59.69 kDa
Atom Count: 3,617
Modeled Residue Count: 420
Deposited Residue Count: 493
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FANCONI ANEMIA GROUP M PROTEIN	A	254	Homo sapiens	Mutation(s): 0 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYD8 (Homo sapiens) Explore Q8IYD8 Go to UniProtKB: Q8IYD8
PHAROS: Q8IYD8 GTEx: ENSG00000187790
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IYD8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FANCONI ANEMIA-ASSOCIATED PROTEIN OF 24 KDA	B	217	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BTP7 (Homo sapiens) Explore Q9BTP7 Go to UniProtKB: Q9BTP7
PHAROS: Q9BTP7 GTEx: ENSG00000131944
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BTP7
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
5'-D(TPCPAPGPCPAPTPCPAPTP*CP)-3'	C [auth H]	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
5'-D(GPAPTPGPAPTPGPCPTPGP*CP)-3'	D [auth I]	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.255 (Depositor), 0.281 (DCC)
R-Value Work: 0.204 (Depositor), 0.223 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.1	α = 90
b = 125.1	β = 90
c = 74.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
BNP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2013-09-25
Changes: Database references
Version 1.2: 2017-06-28
Changes: Data collection
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other