PDB-3s4z: Structure of a Y DNA-FANCI complex

ID or keywords:

Entry

Database: PDB / ID: 3s4z

Title

Structure of a Y DNA-FANCI complex

Components

dna repair 1

Keywords

DNA BINDING PROTEIN / DNA repair

Function / homology

Function and homology information

Fanconi Anemia Pathway / DNA repair complex / DNA polymerase binding / positive regulation of protein ubiquitination / DNA repair / nucleoplasm / cytosol / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 7.8 Å

Authors

Pavletich, N.P.

Citation

Journal: Science / Year: 2011
Title: Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway.
Authors: Joo, W. / Xu, G. / Persky, N.S. / Smogorzewska, A. / Rudge, D.G. / Buzovetsky, O. / Elledge, S.J. / Pavletich, N.P.

History

Deposition	May 20, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2011	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s4z.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb3s4z.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	3s4z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3s4z_validation.pdf.gz	498.4 KB	Display	wwPDB validaton report
Full document	3s4z_full_validation.pdf.gz	712.1 KB	Display
Data in XML	3s4z_validation.xml.gz	130.9 KB	Display
Data in CIF	3s4z_validation.cif.gz	172.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s4/3s4z ftp://data.pdbj.org/pub/pdb/validation_reports/s4/3s4z	HTTPS FTP

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Related structure data

Related structure data	3s4wC 3s51C C: citing same article (ref.)
Similar structure data	3s51-1 3s51-3 1eo8-d 3k38-1 1qfu-d 4lqq-d 4idv-d 9035 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3s4wC

3s51C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: dna repair 1

B: dna repair 1

C: dna repair 1

441 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: dna repair 1

defined by author
147 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: dna repair 1

defined by author
147 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: dna repair 1

defined by author
147 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	235.200, 307.900, 375.900
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

#1: Protein	dna repair 1 Mass: 147120.562 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8K368

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density % sol: 78.4 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 50 mM Hepes-Na, 10 mM DTT, 2.5 mM EDTA, 9 to 11 % (w/v) PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 12, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 7.8→50 Å / Num. all: 15802 / Num. obs: 14728 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 7.8→33 Å / Cor.coef. F_o:F_c: 0.784 / Cor.coef. F_o:F_c free: 0.804 / SU ML: 3.394 / Cross valid method: THROUGHOUT / ESU R Free: 3.929 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: In addition to the 3 polypeptide chains, the asymmetric unit also contains 3 copies of DNA (23,760 Da per DNA = 71,280 Da total). When the DNA is included (509750 Da per au), authors ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.32431	544	4.1 %	RANDOM
R_work	0.30967	-	-	-
all	0.31	15045	-	-
obs	0.31023	12837	85.32 %	-

Solvent computation

Ion probe radii: 1.4 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 246.447 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-12.68 Å²	0 Å²	0 Å²
2-	-	15.79 Å²	0 Å²
3-	-	-	-3.11 Å²

Refinement step

Cycle: LAST / Resolution: 7.8→33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26814	0	0	0	26814

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.022	27522
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.035	1.986	37176
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.673	5	3405
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.53	24.717	1113
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.093	15	5208
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.066	15	129
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	4488
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	19683
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 7.8→7.991 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.454	26	-
R_work	0.407	562	-
obs	-	-	54.04 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.1186	1.9585	0.1173	2.6837	0.565	3.8583	-1.2309	-0.3459	0.4323	-1.5416	0.6685	-1.0938	0.5296	1.002	0.5624	2.3221	-0.1254	0.0023	3.1312	0.1168	2.711	-14.2641	87.4955	-37.643
2	20.0386	10.4477	-15.3759	4.932	-7.8601	20.5823	-0.2264	0.6027	0.6489	0.1007	0.5152	0.01	-2.2683	1.478	-0.2888	1.6419	0.4111	-1.219	1.9016	0.8116	1.5957	-19.4134	74.8721	-16.8495
3	5.1738	-2.781	-1.3127	5.7792	-2.8585	3.2947	-0.0813	-0.0206	0.5974	0.347	-0.5934	-0.5505	0.0335	-0.1713	0.6747	2.1515	-0.0756	-1.1429	1.0038	-0.608	0.9898	-47.8298	71.8822	12.9291
4	4.2753	-1.2288	2.5035	3.6927	0.727	4.0299	-0.6821	-0.1469	0.2991	-0.6932	0.3047	-0.274	-0.3465	-0.9002	0.3774	1.7432	-0.2205	0.1203	2.0221	-0.3803	2.3552	-78.7596	75.3218	48.5389
5	14.2852	-7.8339	-6.1548	7.6925	-4.2505	16.765	0.2433	-0.232	-0.0635	0.0803	-0.3404	0.4006	1.0006	0.0545	0.0971	1.725	-0.5477	-0.5573	0.5648	-0.9121	1.5869	-52.166	62.7223	53.9259
6	25.1209	10.9702	-2.848	34.1307	12.1952	6.083	1.024	1.1807	-1.7372	0.8767	-1.4367	0.0311	0.1686	0.3784	0.4127	1.2626	0.6454	-1.1128	2.1168	-0.1822	0.8764	-36.5752	48.7256	45.7586
7	9.577	0.829	-0.3471	11.232	1.7744	6.572	1.5175	-0.0383	1.4388	0.8171	0.025	0.6961	0.5148	1.775	-1.5425	1.5339	0.9027	-0.18	1.3398	-0.0889	1.3617	-29.2986	33.4982	23.3985
8	11.6257	-1.3708	-5.7535	-4.6335	1.1515	-1.3308	0.6435	1.1634	-1.465	-0.2251	-1.4533	0.4324	-0.5832	-0.4271	0.8098	4.4939	0.5297	0.0132	3.9205	-0.3517	3.3299	-7.1733	-56.3624	51.362
9	0.0305	1.0194	1.6733	1.1599	2.161	1.9088	-0.0408	0.761	-0.5342	-0.115	0.0817	-0.2384	0.9353	-0.0182	-0.0409	3.5608	0.9448	0.1841	3.1828	0.3548	2.0822	-8.3806	-31.5275	50.4239
10	1.0706	1.1501	1.9509	7.0604	3.1875	3.8319	0.3316	-0.1233	0.3114	-0.4322	-0.405	-0.2144	0.6662	0.0457	0.0734	1.7066	0.6523	0.2303	2.0803	1.0365	1.2143	3.1432	2.6412	70.1709
11	2.3101	0.3216	1.0278	3.5538	-0.3647	0.6156	0.6627	-1.3002	0.2325	0.3524	-1.4492	-0.1256	0.0126	-0.1351	0.7865	2.0989	0.1331	-0.2291	1.8193	0.8234	1.6383	13.8961	39.0793	99.2604
12	0.7367	3.6099	1.7619	15.9085	0.5418	5.6202	0.0482	0.0591	0.2866	-0.6674	-0.5323	0.4601	-0.266	-0.1412	0.4841	1.1288	0.1828	0.0054	2.1279	0.3528	0.7075	-8.2167	42.7241	79.7895
13	4.2978	3.9945	-4.1258	29.1179	-2.9406	18.5933	-0.5046	-0.8278	1.9894	-0.0911	-0.1599	1.8377	0.6807	0.2304	0.6645	0.7679	0.8458	-0.7671	2.0905	0.0321	1.9921	-14.54	38.8768	58.562
14	5.211	1.984	-4.388	7.6254	-1.4613	4.803	1.3463	0.7381	0.0954	0.5437	-2.4166	1.142	-0.1678	-0.2071	1.0704	2.3978	0.7305	-0.4388	2.1979	0.2345	0.9491	-7.6965	25.4888	34.6268
15	5.77	-3.2336	-1.7428	-1.4893	0.4313	-2.4795	-0.5275	-3.6619	-0.8135	-0.5886	1.2827	0.7806	0.1687	1.4434	-0.7553	4.11	-0.2166	-0.642	2.4427	-0.9165	5.6789	57.7416	46.9181	144.5047
16	3.2572	-5.3852	-3.2199	12.025	5.2659	16.6011	-0.6938	-0.4086	-0.0393	1.074	-0.0391	1.0557	0.5679	0.6863	0.733	1.8176	-0.0865	0.6372	2.263	0.2424	3.6361	57.5698	47.2824	119.6494
17	-0.0906	0.715	0.8827	1.0846	1.1068	1.0189	0.2127	-0.2666	-0.2318	-0.1417	-0.5529	-0.6012	-0.1175	-0.5521	0.3402	2.2884	0.0175	0.3701	2.1428	1.4109	2.7354	46.34	22.9761	88.1917
18	2.2506	1.6437	0.3136	1.7814	1.2829	-0.7738	0.8706	0.9528	-0.8039	-0.4095	-0.0155	-1.3376	-0.2432	-0.3545	-0.8551	2.4357	0.6325	0.6679	2.8114	1.3869	1.7118	35.491	-9.708	55.5188
19	1.4074	3.0491	-0.1619	3.5923	-0.7315	1.7358	-0.9265	-0.0038	-0.1218	-0.4851	0.3947	0.1494	0.5305	1.0415	0.5318	2.6545	1.1002	1.0845	2.0939	1.1357	2.5471	57.2639	9.2669	49.2144
20	2.2285	2.4386	10.2925	25.5658	1.3805	22.3733	0.4692	1.4245	-0.4285	-0.9274	-0.6093	-0.9618	2.6482	3.5715	0.1401	1.3186	0.4834	1.0814	2.9602	1.1299	1.7111	63.1802	30.9324	50.5765
21	2.5345	-3.1808	3.1311	5.4016	0.4557	15.2901	1.4301	0.8389	0.1196	-0.5254	0.3257	-1.402	0.8171	2.5914	-1.7557	1.8963	-0.2983	0.3936	1.7245	0.7247	2.1971	55.3683	55.8074	60.7041

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 119
2	X-RAY DIFFRACTION	2	A	120 - 224
3	X-RAY DIFFRACTION	3	A	225 - 508
4	X-RAY DIFFRACTION	4	A	509 - 784
5	X-RAY DIFFRACTION	5	A	798 - 970
6	X-RAY DIFFRACTION	6	A	971 - 1035
7	X-RAY DIFFRACTION	7	A	1039 - 1280
8	X-RAY DIFFRACTION	8	B	1 - 119
9	X-RAY DIFFRACTION	9	B	120 - 224
10	X-RAY DIFFRACTION	10	B	225 - 508
11	X-RAY DIFFRACTION	11	B	509 - 784
12	X-RAY DIFFRACTION	12	B	798 - 970
13	X-RAY DIFFRACTION	13	B	971 - 1035
14	X-RAY DIFFRACTION	14	B	1039 - 1280
15	X-RAY DIFFRACTION	15	C	1 - 119
16	X-RAY DIFFRACTION	16	C	120 - 224
17	X-RAY DIFFRACTION	17	C	225 - 508
18	X-RAY DIFFRACTION	18	C	509 - 784
19	X-RAY DIFFRACTION	19	C	798 - 970
20	X-RAY DIFFRACTION	20	C	971 - 1035
21	X-RAY DIFFRACTION	21	C	1039 - 1280

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