PDB-5uek: Structure of antigen-Fab 12E complex with Histone chaperone ASF1

ID or keywords:

Entry

Database: PDB / ID: 5uek

Title

Structure of antigen-Fab 12E complex with Histone chaperone ASF1

Components

Fab 12E Heavy Chain
Fab 12E Light Chain
Histone chaperone ASF1

Keywords

IMMUNE SYSTEM / Antibody / Fab / Asf1 / histone chaperone

Function / homology

Function and homology information

Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / nucleosome disassembly / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.7 Å

Authors

Bailey, L.J. / Kossiakoff, A.A.

Citation

Journal: To Be Published
Title: Antibody Switch Residue Engineering for Improved Crystallization Chaperones
Authors: Bailey, L.J. / Kossiakoff, A.A.

History

Deposition	Jan 2, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uek.cif.gz	249.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5uek.ent.gz	198.9 KB	Display	PDB format
PDBx/mmJSON format	5uek.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5uek_validation.pdf.gz	435.3 KB	Display	wwPDB validaton report
Full document	5uek_full_validation.pdf.gz	436.2 KB	Display
Data in XML	5uek_validation.xml.gz	32.4 KB	Display
Data in CIF	5uek_validation.cif.gz	45.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ue/5uek ftp://data.pdbj.org/pub/pdb/validation_reports/ue/5uek	HTTPS FTP

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Related structure data

Related structure data	5ucbC 5ueaC C: citing same article (ref.)
Similar structure data	5ucb-d 6ayz-1 4rrp-3 6az2-1 6ayz-2 5uea-1 4rrp-5 5eii-2 6az2-2 4rrp-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Histone chaperone ASF1

H: Fab 12E Heavy Chain

L: Fab 12E Light Chain

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	43.175, 142.932, 49.401
Angle α, β, γ (deg.)	90.00, 98.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1 Mass: 17428.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: ASF1, CIA1, YJL115W, J0755 / Production host: Escherichia coli (E. coli) / References: UniProt: P32447
#2: Antibody	Fab 12E Heavy Chain Mass: 24170.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody	Fab 12E Light Chain Mass: 23355.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 20% ethylene glycol, .2 M Ammonium Acetate

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.7→22.46 Å / Num. obs: 64692 / % possible obs: 81.4 % / Redundancy: 1.4 % / Net I/σ(I): 22.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Resolution: 1.7→22.458 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2125	2689	5.1 %
R_work	0.1763	-	-
obs	0.1782	52746	81.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→22.458 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4431	0	0	591	5022

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4549
X-RAY DIFFRACTION	f_angle_d	0.832	6205
X-RAY DIFFRACTION	f_dihedral_angle_d	3.016	2993
X-RAY DIFFRACTION	f_chiral_restr	0.055	704
X-RAY DIFFRACTION	f_plane_restr	0.005	794

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7002-1.7311	0.2768	135	0.2339	2736	X-RAY DIFFRACTION	84
1.7311-1.7643	0.2771	142	0.2337	2734	X-RAY DIFFRACTION	85
1.7643-1.8003	0.2714	137	0.2211	2746	X-RAY DIFFRACTION	84
1.8003-1.8395	0.2934	133	0.2158	2645	X-RAY DIFFRACTION	82
1.8395-1.8822	0.2601	138	0.2059	2625	X-RAY DIFFRACTION	81
1.8822-1.9293	0.2338	136	0.2059	2495	X-RAY DIFFRACTION	78
1.9293-1.9814	0.2321	134	0.201	2449	X-RAY DIFFRACTION	76
1.9814-2.0397	0.2516	126	0.202	2463	X-RAY DIFFRACTION	76
2.0397-2.1055	0.2373	156	0.2004	2442	X-RAY DIFFRACTION	77
2.1055-2.1807	0.2499	151	0.1929	2429	X-RAY DIFFRACTION	76
2.1807-2.2679	0.2471	133	0.1943	2592	X-RAY DIFFRACTION	80
2.2679-2.371	0.2534	142	0.189	2590	X-RAY DIFFRACTION	80
2.371-2.4959	0.2403	148	0.1923	2622	X-RAY DIFFRACTION	82
2.4959-2.652	0.2281	132	0.191	2695	X-RAY DIFFRACTION	83
2.652-2.8564	0.2251	157	0.1875	2712	X-RAY DIFFRACTION	84
2.8564-3.1432	0.2063	140	0.1773	2567	X-RAY DIFFRACTION	80
3.1432-3.5964	0.1821	143	0.1611	2656	X-RAY DIFFRACTION	82
3.5964-4.525	0.1818	153	0.1396	2832	X-RAY DIFFRACTION	88
4.525-22.4596	0.1663	153	0.1542	3027	X-RAY DIFFRACTION	92

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	5.8156	7.0383	5.0198	8.4852	6.1364	4.4287	-0.337	0.5532	0.1699	-0.3299	0.207	0.1249	-0.1184	0.1487	0.2133	0.2518	-0.0035	0.0355	0.297	-0.0026	0.2985	-3.8625	-40.6108	6.0906
2	5.5404	2.9561	4.0951	3.0173	2.4457	3.7414	0.0319	0.0488	-0.4957	0.0508	0.1812	-0.3907	-0.0071	0.0944	-0.2379	0.1646	0.0155	0.0192	0.1833	0.0171	0.2539	-9.7657	-46.2515	8.6904
3	3.1931	-1.9717	4.333	3.0625	-2.4704	5.929	-0.469	-0.6539	0.49	0.1796	0.4364	0.4533	-0.4201	-0.7924	0.1335	0.2334	0.0224	0.0001	0.25	0.0281	0.301	-23.1943	-37.969	8.6757
4	3.0167	-0.5894	4.6822	1.5445	-0.3407	7.8024	0.1567	0.0376	0.0637	0.0867	-0.1186	-0.0282	-0.4646	-0.059	0.0024	0.2609	-0.0219	0.0049	0.1979	0.0546	0.2141	-19.3978	-43.0994	14.0243
5	2.2412	0.8773	0.7142	1.5545	0.1163	1.0516	-0.1036	-0.0666	-0.2504	-0.0637	0.1521	0.037	-0.0053	-0.0665	-0.072	0.1581	0.0054	0.012	0.1691	0.0224	0.1932	-17.4744	-42.5972	7.2481
6	7.1581	0.6945	1.5419	2.1591	1.5696	4.021	0.2997	0.6081	-1.0016	-0.4202	-0.1412	0.2909	0.1094	-0.3116	-0.0923	0.3506	-0.0225	-0.0707	0.2643	-0.0678	0.4018	-32.2136	-52.6371	-6.8629
7	4.3413	2.3566	3.8149	3.0794	2.4203	3.512	-0.1261	0.0096	-0.0452	-0.1108	0.1123	-0.116	-0.209	0.1145	-0.0101	0.1691	0.012	0.0363	0.1585	0.0016	0.1325	-8.5691	-33.1802	6.4787
8	1.5081	0.1886	0.0247	1.2753	-1.3829	4.4561	0.0671	-0.1361	-0.0438	-0.0645	-0.1355	-0.0633	0.0399	0.4172	0.0565	0.1414	0.0311	0.024	0.2101	-0.0119	0.1907	-1.0679	-24.1807	-12.0727
9	1.8431	0.5362	-0.4105	2.5664	0.6076	1.0583	0.05	0.09	-0.0114	-0.2242	0.0521	0.0979	-0.03	-0.0653	-0.0997	0.1785	0.0099	0.0113	0.1673	-0.006	0.1004	-11.4655	-27.1717	-12.3788
10	2.7602	-0.5878	1.4489	2.3637	-0.4881	4.5671	0.1492	0.0054	-0.059	-0.2656	0.0138	-0.0996	0.3459	0.0338	-0.1663	0.2164	-0.0022	0.0212	0.1917	-0.0221	0.1711	-4.4533	-30.369	-16.6423
11	0.9198	0.3263	-1.2364	1.3195	-1.4478	2.7244	0.1122	0.0365	0.0018	-0.0529	-0.0454	0.061	-0.1157	0.0756	-0.0695	0.1998	0.0235	0.0009	0.1883	-0.0041	0.1487	-9.8047	-22.2887	-11.8837
12	0.8542	-1.1044	-0.2294	3.8124	0.383	1.6427	0.1258	0.0389	0.0979	-0.3537	-0.2103	0.0561	-0.1894	-0.0412	0.0842	0.1364	-0.0103	-0.0162	0.1966	-0.026	0.1834	-11.1108	3.7846	-27.4186
13	0.9572	-0.0035	-0.121	2.096	0.6041	1.4383	0.0112	-0.0582	-0.0043	-0.0406	-0.0086	0.028	0.013	0.0789	-0.0135	0.157	0.0226	0.005	0.1562	-0.01	0.1588	-11.1379	5.762	-23.3056
14	3.4215	-1.2266	-1.1122	2.6607	2.9005	3.0108	0.0501	0.1383	0.1469	-0.1973	0.1252	-0.627	-0.0581	0.2181	-0.2394	0.2125	-0.0109	0.0023	0.2175	-0.0143	0.2497	-3.1383	10.7591	-26.2079
15	2.0786	-0.3817	-0.2207	5.9778	2.6428	3.1812	0.2552	0.1938	-0.3999	-0.6358	-0.5326	0.6081	-0.2538	-0.5661	0.1886	0.2698	0.0298	-0.0677	0.2914	-0.0182	0.2876	-28.9598	-13.5922	-7.8584
16	1.9595	0.9	0.3052	1.0211	-0.7041	1.735	-0.0132	0.1132	-0.2177	-0.0731	0.0534	0.1069	0.1988	-0.1849	-0.0281	0.1904	0.0139	0.0247	0.2336	-0.0214	0.2636	-29.8556	-17.0465	-0.9843
17	2.0467	-0.7228	-0.2442	3.0905	-1.1243	2.9789	0.1292	0.0067	0.0143	-0.0306	-0.1164	-0.1861	-0.2869	0.0626	-0.0174	0.1685	0.0225	0.034	0.1467	0.0022	0.1744	-16.9719	-16.9912	-2.4529
18	0.8643	-0.057	-0.0254	2.1785	0.8109	1.5784	0.0128	-0.1109	-0.0546	0.1271	-0.0645	0.0779	0.0268	-0.126	0.0552	0.142	-0.0049	0.0085	0.1609	-0.0001	0.1583	-23.79	-19.8295	4.6436
19	0.9787	-1.0054	-0.6679	3.5358	1.6628	2.1246	0.1295	0.0181	0.0139	-0.2332	-0.1384	-0.1988	-0.1812	-0.1427	-0.0114	0.1716	0.0197	0.0174	0.1894	0.0078	0.1848	-21.3294	-12.1816	-1.0067
20	0.6411	0.0422	0.0131	1.8337	-0.4766	0.502	0.0842	0.0932	-0.0195	0.185	-0.1514	0.2767	0.0231	-0.1437	0.0768	0.1719	0.0081	0.0142	0.1533	-0.0061	0.1314	-24.277	-10.8484	-8.3719
21	3.9312	-2.1687	-4.266	2.6256	4.2183	7.0509	0.2378	0.1264	0.1567	-0.4318	-0.0778	-0.1689	-0.3678	0.1187	-0.1568	0.27	0.0301	-0.0212	0.1937	0.035	0.2793	-17.0416	12.303	-33.3727
22	0.8189	0.6463	-1.2241	1.2491	0.1638	8.9036	-0.0897	-0.0622	0.0061	-0.1956	0.0204	0.3122	0.3486	-0.1461	0.0924	0.2041	0.0271	-0.0088	0.1378	-0.0031	0.2889	-26.6677	7.5963	-22.7639
23	4.3053	-0.6377	3.2432	1.4435	-2.0517	7.4166	-0.1478	-0.0597	0.1481	-0.2009	0.2282	0.3076	-0.0777	-0.5703	-0.0614	0.2679	-0.0097	-0.0498	0.1893	-0.0061	0.3446	-29.2198	4.7143	-31.1851
24	1.1115	-0.0117	-0.1331	2.5501	-0.6185	9.5265	-0.0284	0.0448	0.1099	-0.0801	-0.0849	0.0673	0.0417	0.1987	0.0821	0.1311	0.0144	-0.0084	0.1228	-0.0009	0.2177	-21.4266	6.3669	-24.7271
25	2.0316	0.2217	-1.8787	2.4757	-0.944	2.3653	0.2413	0.042	0.4075	-0.0557	0.163	0.5072	-0.3878	-0.2423	-0.512	0.1885	0.0408	-0.0034	0.2026	0.0361	0.3892	-30.4191	14.968	-26.7982

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:11 )	A	2 - 11
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 12:37 )	A	12 - 37
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 38:52 )	A	38 - 52
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 53:62 )	A	53 - 62
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 63:117 )	A	63 - 117
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 118:139 )	A	118 - 139
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 140:154 )	A	140 - 154
8	X-RAY DIFFRACTION	8	( CHAIN H AND RESID 1:33 )	H	1 - 33
9	X-RAY DIFFRACTION	9	( CHAIN H AND RESID 34:59 )	H	34 - 59
10	X-RAY DIFFRACTION	10	( CHAIN H AND RESID 60:82 )	H	60 - 82
11	X-RAY DIFFRACTION	11	( CHAIN H AND RESID 83:106 )	H	83 - 106
12	X-RAY DIFFRACTION	12	( CHAIN H AND RESID 107:134 )	H	107 - 134
13	X-RAY DIFFRACTION	13	( CHAIN H AND RESID 135:188 )	H	135 - 188
14	X-RAY DIFFRACTION	14	( CHAIN H AND RESID 189:214 )	H	189 - 214
15	X-RAY DIFFRACTION	15	( CHAIN L AND RESID 3:13 )	L	3 - 13
16	X-RAY DIFFRACTION	16	( CHAIN L AND RESID 14:29 )	L	14 - 29
17	X-RAY DIFFRACTION	17	( CHAIN L AND RESID 30:48 )	L	30 - 48
18	X-RAY DIFFRACTION	18	( CHAIN L AND RESID 49:75 )	L	49 - 75
19	X-RAY DIFFRACTION	19	( CHAIN L AND RESID 76:91 )	L	76 - 91
20	X-RAY DIFFRACTION	20	( CHAIN L AND RESID 92:113 )	L	92 - 113
21	X-RAY DIFFRACTION	21	( CHAIN L AND RESID 114:128 )	L	114 - 128
22	X-RAY DIFFRACTION	22	( CHAIN L AND RESID 129:150 )	L	129 - 150
23	X-RAY DIFFRACTION	23	( CHAIN L AND RESID 151:163 )	L	151 - 163
24	X-RAY DIFFRACTION	24	( CHAIN L AND RESID 164:188 )	L	164 - 188
25	X-RAY DIFFRACTION	25	( CHAIN L AND RESID 189:211 )	L	189 - 211

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Yorodumi