6SRI | pdb_00006sri

Structure of the Fanconi anaemia core complex

• PDB DOI: https://doi.org/10.2210/pdb6SRI/pdb
• EM Map EMD-10290: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Gallus gallus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-09-05 Released: 2019-11-06 
• Deposition Author(s): Shakeel, S., Rajendra, E., Alcon, P., He, S., Scheres, S.H.W., Passmore, L.A.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the Fanconi anaemia monoubiquitin ligase complex.

Shakeel, S., Rajendra, E., Alcon, P., O'Reilly, F., Chorev, D.S., Maslen, S., Degliesposti, G., Russo, C.J., He, S., Hill, C.H., Skehel, J.M., Scheres, S.H.W., Patel, K.J., Rappsilber, J., Robinson, C.V., Passmore, L.A.

(2019) Nature 575: 234-237

• PubMed: 31666700 
• DOI: https://doi.org/10.1038/s41586-019-1703-4
• Primary Citation Related Structures: 
  6SRI, 6SRS


• PubMed Abstract: 
  

  The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress ^1,2 . Genetic inactivation of this pathway by mutation of genes encoding FA complementation group (FANC) proteins impairs development, prevents blood production and promotes cancer ^1,3 . The key molecular step in the FA pathway is the monoubiquitination of a pseudosymmetric heterodimer of FANCD2-FANCI ^4,5 by the FA core complex-a megadalton multiprotein E3 ubiquitin ligase ^6,7 . Monoubiquitinated FANCD2 then recruits additional protein factors to remove the DNA crosslink or to stabilize the stalled replication fork. A molecular structure of the FA core complex would explain how it acts to maintain genome stability. Here we reconstituted an active, recombinant FA core complex, and used cryo-electron microscopy and mass spectrometry to determine its structure. The FA core complex comprises two central dimers of the FANCB and FA-associated protein of 100 kDa (FAAP100) subunits, flanked by two copies of the RING finger subunit, FANCL. These two heterotrimers act as a scaffold to assemble the remaining five subunits, resulting in an extended asymmetric structure. Destabilization of the scaffold would disrupt the entire complex, resulting in a non-functional FA pathway. Thus, the structure provides a mechanistic basis for the low numbers of patients with mutations in FANCB, FANCL and FAAP100. Despite a lack of sequence homology, FANCB and FAAP100 adopt similar structures. The two FANCL subunits are in different conformations at opposite ends of the complex, suggesting that each FANCL has a distinct role. This structural and functional asymmetry of dimeric RING finger domains may be a general feature of E3 ligases. The cryo-electron microscopy structure of the FA core complex provides a foundation for a detailed understanding of its E3 ubiquitin ligase activity and DNA interstrand crosslink repair.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Cambridge, UK.
Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
MRC Laboratory of Molecular Biology, Cambridge, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 47-mer - A10B8C6D6E5F4G3H2I1J1K1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 47-mer - A5B5C2D2E2F2G2H2I2J2K2L2M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - H2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2F2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 375.47 kDa 
• Atom Count: 15,308 
• Modeled Residue Count: 3,827 
• Deposited Residue Count: 4,145 
• Unique protein chains: 27

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100: chain A,a; base region, proposed FANCC-FANC-E-FANCF: chain 3)	A, LA [auth 3], M [auth a]	76	Gallus gallus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	B, N [auth b]	25	Gallus gallus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	C, O [auth c]	30	Gallus gallus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	D, P [auth d]	23	Gallus gallus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	E, Q [auth e]	9	Gallus gallus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100: chain F,f; base region, proposed FANCC-FANC-E-FANCF: chain Z)	F, NA [auth Z], R [auth f]	15	Gallus gallus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	G, S [auth g]	26	Gallus gallus	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	H, J, T [auth h], V [auth j]	17	Gallus gallus	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	I, U [auth i]	37	Gallus gallus	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	K, W [auth k]	21	Gallus gallus	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)	L, X [auth l]	18	Gallus gallus	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (proposed FANCB)	AA [auth m], Y [auth M]	120	Gallus gallus	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (proposed FAAP100)	BA [auth n], Z [auth N]	43	Gallus gallus	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (proposed FANCB)	CA [auth o], QA [auth O]	279	Gallus gallus	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (proposed FAAP100)	DA [auth p], RA [auth P]	276	Gallus gallus	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	EA [auth U]	227	Gallus gallus	Mutation(s): 0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	FA [auth V]	27	Gallus gallus	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	GA [auth W]	20	Gallus gallus	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	HA [auth X]	13	Gallus gallus	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	IA [auth Y]	84	Gallus gallus	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	JA [auth 1]	109	Gallus gallus	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	KA [auth 2]	62	Gallus gallus	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (base region, proposed FANCC-FANC-E-FANCF)	MA [auth 4]	71	Gallus gallus	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Fanconi anaemia protein FANCL	OA [auth q], UA [auth Q]	373	Gallus gallus	Mutation(s): 0  Gene Names: FANCL EC: 2.3.2.27
UniProt
Find proteins for Q3MUH5 (Gallus gallus) Explore Q3MUH5  Go to UniProtKB:  Q3MUH5

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
base region, proposed FANCF	PA [auth T]	201	Gallus gallus	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (top region, proposed FANCG)	SA [auth R]	285	Gallus gallus	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure elements (top region, proposed FANCG)	TA [auth S]	145	Gallus gallus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	REFMAC
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Shakeel, S., Rajendra, E., Alcon, P., He, S., Scheres, S.H.W., Passmore, L.A.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_U105192715

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Database references
• Version 1.3: 2024-05-22
  Changes: Data collection, Database references