PDB-6mii: Crystal structure of minichromosome maintenance protein MCM/DNA c...

ID or keywords:

Entry

Database: PDB / ID: 6mii

Title

Crystal structure of minichromosome maintenance protein MCM/DNA complex

Components

DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Minichromosome maintenance protein MCM

Keywords

HYDROLASE/DNA / MCM / DNA / helicase / AAA+ / HYDROLASE-DNA complex

Function / homology

Function and homology information

MCM complex / single-stranded DNA binding / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.15 Å

Authors

Enemark, E.J. / Meagher, M. / Epling, L.B.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2019
Title: DNA translocation mechanism of the MCM complex and implications for replication initiation.
Authors: Meagher, M. / Epling, L.B. / Enemark, E.J.

History

Deposition	Sep 19, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 31, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6mii.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb6mii.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	6mii.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mi/6mii ftp://data.pdbj.org/pub/pdb/validation_reports/mi/6mii	HTTPS FTP

-
Related structure data

Related structure data	2vl6S 4r7yS S: Starting model for refinement
Similar structure data	10771 4624 6w22-d 6oay-d 8697 6w24-d 5vc7-d 6w23-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#255 - Mar 2021 Cisplatin and DNA similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (12) #150 - Jun 2012 Sliding Clamps similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #23 - Nov 2001 DNA similarity (2) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#255 - Mar 2021
Cisplatin and DNA
similarity (2)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (12)
#150 - Jun 2012
Sliding Clamps
similarity (2)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#23 - Nov 2001
DNA
similarity (2)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Minichromosome maintenance protein MCM

B: Minichromosome maintenance protein MCM

C: Minichromosome maintenance protein MCM

D: Minichromosome maintenance protein MCM

E: Minichromosome maintenance protein MCM

F: Minichromosome maintenance protein MCM

X: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

hetero molecules

419 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, The MCM complex forms a well-established hexameric ring.

Unit cell

Length a, b, c (Å)	186.665, 186.665, 281.489
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

-
Protein / DNA chain , 2 types, 7 molecules ABCDEFX

#1: Protein	Minichromosome maintenance protein MCM Mass: 68641.961 Da / Num. of mol.: 6 Mutation: UNP residues 2-265, GGSGGS linker, UNP residues 275-612 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: MCM, SSO0774 / Plasmid: pEE078.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q9UXG1, DNA helicase
#2: DNA chain	DNA (5'-D(PTPTPTPTPTPTPTPTPTPT)-3') Mass: 3605.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#1: Protein

Minichromosome maintenance protein MCM

Mass: 68641.961 Da / Num. of mol.: 6
Mutation: UNP residues 2-265, GGSGGS linker, UNP residues 275-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: MCM, SSO0774 / Plasmid: pEE078.1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q9UXG1, DNA helicase

#2: DNA chain

DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

Mass: 3605.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 36 molecules

#3: Chemical	ChemComp-08T / [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium Mass: 492.201 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₁₀H₁₄BeF₃N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.3 % / Description: long tetragonal rod
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM MES, pH 6.0, 100 mM sodium chloride, 20 mM magnesium chloride, 9% PEG8000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 26, 2017
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.15→50 Å / Num. obs: 84725 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / R_merge(I) obs: 0.119 / R_pim(I) all: 0.125 / R_rim(I) all: 0.036 / Χ²: 0.743 / Net I/σ(I): 17.6
Reflection shell	Resolution: 3.15→3.26 Å / Redundancy: 4.5 % / R_merge(I) obs: 1.789 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7600 / CC_1/2: 0.245 / R_pim(I) all: 0.877 / R_rim(I) all: 2.007 / Χ²: 0.515 / % possible all: 89.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 4R7Y & 2VL6

4r7y

2vl6

Resolution: 3.15→44.698 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.83

	R_factor	Num. reflection	% reflection
R_free	0.2413	4259	5.06 %
R_work	0.1881	-	-
obs	0.1908	84156	96.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.15→44.698 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28089	201	186	18	28494

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	29024
X-RAY DIFFRACTION	f_angle_d	1.044	39349
X-RAY DIFFRACTION	f_dihedral_angle_d	5.38	17932
X-RAY DIFFRACTION	f_chiral_restr	0.058	4519
X-RAY DIFFRACTION	f_plane_restr	0.006	4974

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 (%)
3.1436-3.1793	0.3773	83	0.3568	1581	X-RAY DIFFRACTION	59
3.1793-3.2167	0.3926	119	0.3434	2357	X-RAY DIFFRACTION	86
3.2167-3.2559	0.3761	147	0.3217	2430	X-RAY DIFFRACTION	92
3.2559-3.2971	0.3671	128	0.3054	2619	X-RAY DIFFRACTION	96
3.2971-3.3405	0.3364	163	0.2924	2679	X-RAY DIFFRACTION	98
3.3405-3.3862	0.3388	132	0.282	2681	X-RAY DIFFRACTION	99
3.3862-3.4346	0.3405	144	0.2756	2640	X-RAY DIFFRACTION	99
3.4346-3.4858	0.2836	131	0.2621	2703	X-RAY DIFFRACTION	99
3.4858-3.5403	0.3121	146	0.2477	2683	X-RAY DIFFRACTION	99
3.5403-3.5983	0.2911	158	0.2353	2681	X-RAY DIFFRACTION	99
3.5983-3.6603	0.2769	150	0.2158	2672	X-RAY DIFFRACTION	99
3.6603-3.7268	0.3066	140	0.2136	2678	X-RAY DIFFRACTION	99
3.7268-3.7985	0.2415	160	0.2103	2689	X-RAY DIFFRACTION	99
3.7985-3.876	0.2589	139	0.2085	2690	X-RAY DIFFRACTION	99
3.876-3.9602	0.2665	137	0.2074	2691	X-RAY DIFFRACTION	99
3.9602-4.0523	0.2679	148	0.1906	2712	X-RAY DIFFRACTION	99
4.0523-4.1535	0.2484	136	0.1878	2722	X-RAY DIFFRACTION	99
4.1535-4.2657	0.2206	147	0.1686	2693	X-RAY DIFFRACTION	99
4.2657-4.3912	0.2153	154	0.1674	2701	X-RAY DIFFRACTION	99
4.3912-4.5328	0.2326	128	0.1678	2738	X-RAY DIFFRACTION	99
4.5328-4.6946	0.2363	135	0.1681	2718	X-RAY DIFFRACTION	99
4.6946-4.8823	0.2566	141	0.1676	2745	X-RAY DIFFRACTION	99
4.8823-5.1043	0.2146	165	0.1718	2708	X-RAY DIFFRACTION	99
5.1043-5.3729	0.232	138	0.1736	2761	X-RAY DIFFRACTION	99
5.3729-5.7089	0.2348	149	0.1761	2747	X-RAY DIFFRACTION	99
5.7089-6.1487	0.2742	160	0.1988	2759	X-RAY DIFFRACTION	99
6.1487-6.7656	0.2897	142	0.1966	2781	X-RAY DIFFRACTION	99
6.7656-7.7402	0.2657	150	0.1779	2808	X-RAY DIFFRACTION	100
7.7402-9.7352	0.1652	130	0.1532	2870	X-RAY DIFFRACTION	100
9.7352-44.703	0.1902	159	0.1668	2960	X-RAY DIFFRACTION	99

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	8.5199	-2.3173	0.4711	9.8889	0.429	7.0748	0.0547	0.7795	1.0407	-1.1628	0.3206	-0.2892	-1.0299	1.2538	-0.3239	1.2191	-0.3227	0.222	0.9583	-0.0082	1.0929	99.2462	61.1121	48.0194
2	8.3449	0.2152	-0.4937	9.0907	-3.1077	6.3865	-0.216	-0.1178	0.8784	-0.2371	0.037	-0.4114	0.3957	-0.4412	0.1873	1.0676	-0.2007	0.0745	0.7735	-0.0911	1.1324	81.059	47.7546	58.0624
3	8.8043	3.4941	5.4116	3.2287	0.525	8.5547	-1.3115	-1.7237	0.8975	-0.1695	-1.0353	-0.0791	-0.9619	-0.3206	2.2273	1.5695	-0.033	-0.1318	1.8219	-0.3886	2.0673	88.6847	68.4251	79.2514
4	2.3472	-1.5525	0.6013	3.7583	0.1957	3.2047	-0.1314	-0.1299	-0.2162	0.5377	0.351	0.8282	0.0283	-0.5188	-0.1771	1.0253	0.127	0.4397	0.8731	0.179	1.1928	55.035	50.5272	30.325
5	3.9589	1.1957	-0.2287	5.7696	-1.6277	8.0682	0.1091	-0.4099	-1.1257	0.0955	-0.5721	-1.2913	0.9951	1.3782	0.4626	1.3658	0.2744	0.1087	1.452	0.2664	1.4186	97.5823	14.8845	64.2806
6	8.358	0.2746	-1.9387	2.3395	-2.1773	7.9428	-0.0387	-0.4301	0.0842	0.1034	-0.2512	-0.0969	0.0317	0.461	0.3069	1.2037	0.0214	-0.0491	0.8203	0.0589	0.9016	75.7159	22.8746	72.8846
7	7.8735	1.9722	0.1958	5.1072	3.5987	2.7507	-0.6132	-1.114	1.5141	1.3682	-0.3878	-0.6476	-1.7515	2.5233	0.4008	1.6679	-0.387	-0.5009	1.7793	-0.109	1.3697	95.4483	45.5188	80.1017
8	4.112	1.9484	-1.8156	3.5946	-1.4689	4.1307	0.2754	0.0773	0.3631	-0.0313	0.1393	0.2192	-0.3466	0.023	0.0323	1.114	-0.0273	0.2238	0.5795	-0.046	1.0105	58.0893	16.7883	42.7132
9	9.6376	-2.9373	1.404	6.9772	0.1564	7.4795	0.2261	-0.1676	-0.8511	0.4301	-0.3535	-0.5275	0.412	0.4221	0.1117	1.0245	-0.0434	-0.0566	0.9689	0.2781	0.9088	69.037	3.4472	104.5545
10	6.9663	-1.791	-1.7148	3.8575	1.3232	6.4153	-0.0324	-0.3812	0.0443	0.2594	0.3567	0.2381	-0.2711	0.3808	-0.329	1.346	-0.0703	0.0781	1.0877	0.1532	0.8103	56.8626	22.317	94.9337
11	9.5264	3.8239	-0.1313	9.4872	-0.4079	7.2707	0.5923	-0.2374	0.302	1.7522	-0.7151	-2.4556	-1.0728	1.4888	0.0138	1.6163	-0.444	-0.4096	1.9968	-0.0096	1.5961	86.4121	29.9624	96.0022
12	3.6419	-0.3918	-0.4938	2.9345	0.1842	3.1505	0.3309	-0.3171	0.027	-0.1925	0.031	0.1054	-0.031	-0.313	-0.2742	0.8435	-0.0843	0.1681	0.6976	0.155	0.833	37.4013	5.5392	69.7693
13	4.8553	-1.015	0.1702	5.6092	4.6803	9.594	-0.1301	-1.6443	0.0567	2.0328	0.4401	0.1514	-0.4659	-0.0648	-0.285	2.3257	0.3381	0.3187	1.9526	0.0435	0.9618	39.1857	36.3602	124.866
14	1.8077	-0.2483	0.4926	5.4717	0.7421	4.4091	-0.0245	-0.1373	0.4732	0.7158	0.5797	0.145	-0.1977	-0.5063	-0.5044	1.6505	0.2818	0.1774	1.5498	0.0278	1.0868	42.6045	46.6314	102.4627
15	6.6693	-0.2969	0.1292	4.4528	-0.5746	6.2097	0.3352	-1.0505	0.5987	1.5468	-0.2676	-0.7467	-1.2078	0.856	-0.093	2.2953	-0.3602	-0.2644	2.0314	-0.1244	1.4813	70.8068	37.9072	111.2112
16	3.4808	-0.403	0.1498	3.311	0.5371	2.02	0.0497	-0.1237	-0.0553	0.2811	0.2244	0.2802	-0.1216	-0.7131	-0.2192	1.0275	0.2325	0.3746	1.251	0.2845	0.8834	15.8317	28.3037	86.6707
17	3.6211	-2.5654	2.812	6.346	0.4468	3.4617	0.5748	-0.7192	0.8736	2.4794	-0.1575	1.0128	-1.944	-1.8342	-0.3341	3.3717	0.2648	0.8984	1.7754	-0.0249	1.8716	39.3673	84.5066	107.0728
18	1.7804	2.0672	1.5175	7.117	-2.6488	6.6104	0.2766	0.3287	0.3837	0.9967	0.0526	0.2136	-0.9182	-0.26	-0.4005	2.1507	0.4243	0.3312	1.6095	0.1461	1.9564	47.1705	71.1711	87.4917
19	6.9869	0.629	3.3666	2.2707	1.4509	4.6079	0.1016	-0.4473	-0.4299	0.1953	0.4589	-1.4979	-0.3085	0.3773	-0.5302	2.465	0.0456	-0.1791	1.6275	-0.2916	2.0783	63.5337	60.4759	111.588
20	2.0695	-0.0124	-0.4698	4.5311	-1.1983	1.7299	0.2156	0.1432	0.6479	0.4682	0.1411	0.5219	-0.5063	-0.7163	-0.168	1.6268	0.5798	0.6084	1.5605	0.3607	1.4769	14.147	62.2461	75.7249
21	1.2934	0.903	-2.2695	2.9666	-3.4966	5.555	1.1254	-0.2914	2.8378	-0.1189	0.6838	-0.6479	-3.3029	0.2006	-0.9215	3.0639	-0.094	0.7548	1.2964	-0.0596	3.0659	66.9435	96.3371	67.451
22	4.7695	-2.5127	-3.0981	1.4598	2.3864	5.8071	0.6308	-0.3825	1.3434	-0.2494	0.3123	-0.8502	-0.7487	-0.6686	-0.9021	1.6122	-0.131	0.2014	0.932	0.2538	1.5954	66.3168	71.6468	64.7809
23	9.1573	2.3653	2.2411	6.6268	4.7113	3.4521	1.9357	-2.035	0.7728	0.9735	0.5057	-1.7984	-0.6281	0.3853	-2.6036	2.7451	-0.5741	0.2503	2.4262	-0.4962	1.9333	72.4119	75.2427	95.0684
24	2.9202	-0.1124	-1.0721	1.5232	-1.0942	4.1103	0.0335	0.053	0.1798	0.2362	0.1459	0.1929	-0.6465	-0.6662	-0.0194	1.7017	0.5723	0.5333	1.1153	0.3209	1.2987	33.5553	73.1881	47.6767
25	3.4783	-0.8672	5.1583	0.2069	-1.2847	7.6539	-0.9183	1.4193	0.541	0.4683	-0	-2.3581	-2.9489	-0.4571	0.3732	2.004	0.1778	0.7835	1.4264	0.3746	1.9032	44.506	40.9793	68.38

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN F AND RESID 7:107 )	F	7 - 107
2	X-RAY DIFFRACTION	2	( CHAIN F AND ( RESID 108:134 OR RESID 190:265 ) )	F	108 - 134
3	X-RAY DIFFRACTION	2	( CHAIN F AND ( RESID 108:134 OR RESID 190:265 ) )	F	190 - 265
4	X-RAY DIFFRACTION	3	( CHAIN F AND ( RESID 135:189 OR RESID 2002:2002 ) )	F	135 - 189
5	X-RAY DIFFRACTION	3	( CHAIN F AND ( RESID 135:189 OR RESID 2002:2002 ) )	F	2002
6	X-RAY DIFFRACTION	4	( CHAIN F AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	F	275 - 604
7	X-RAY DIFFRACTION	4	( CHAIN F AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	F	2001
8	X-RAY DIFFRACTION	4	( CHAIN F AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	F	2003
9	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 7:107 )	A	7 - 107
10	X-RAY DIFFRACTION	6	( CHAIN A AND ( RESID 108:134 OR RESID 190:265 ) )	A	108 - 134
11	X-RAY DIFFRACTION	6	( CHAIN A AND ( RESID 108:134 OR RESID 190:265 ) )	A	190 - 265
12	X-RAY DIFFRACTION	7	( CHAIN A AND ( RESID 135:189 OR RESID 2002:2002 ) )	A	135 - 189
13	X-RAY DIFFRACTION	7	( CHAIN A AND ( RESID 135:189 OR RESID 2002:2002 ) )	A	2002
14	X-RAY DIFFRACTION	8	( CHAIN A AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	A	275 - 604
15	X-RAY DIFFRACTION	8	( CHAIN A AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	A	2001
16	X-RAY DIFFRACTION	8	( CHAIN A AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	A	2003
17	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 7:107 )	B	7 - 107
18	X-RAY DIFFRACTION	10	( CHAIN B AND ( RESID 108:134 OR RESID 190:265 ) )	B	108 - 134
19	X-RAY DIFFRACTION	10	( CHAIN B AND ( RESID 108:134 OR RESID 190:265 ) )	B	190 - 265
20	X-RAY DIFFRACTION	11	( CHAIN B AND ( RESID 135:189 OR RESID 2002:2002 ) )	B	135 - 189
21	X-RAY DIFFRACTION	11	( CHAIN B AND ( RESID 135:189 OR RESID 2002:2002 ) )	B	2002
22	X-RAY DIFFRACTION	12	( CHAIN B AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	B	275 - 604
23	X-RAY DIFFRACTION	12	( CHAIN B AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	B	2001
24	X-RAY DIFFRACTION	12	( CHAIN B AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	B	2003
25	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 7:107 )	C	7 - 107
26	X-RAY DIFFRACTION	14	( CHAIN C AND ( RESID 108:134 OR RESID 190:265 ) )	C	108 - 134
27	X-RAY DIFFRACTION	14	( CHAIN C AND ( RESID 108:134 OR RESID 190:265 ) )	C	190 - 265
28	X-RAY DIFFRACTION	15	( CHAIN C AND ( RESID 135:189 OR RESID 2002:2002 ) )	C	135 - 189
29	X-RAY DIFFRACTION	15	( CHAIN C AND ( RESID 135:189 OR RESID 2002:2002 ) )	C	2002
30	X-RAY DIFFRACTION	16	( CHAIN C AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	C	275 - 604
31	X-RAY DIFFRACTION	16	( CHAIN C AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	C	2001
32	X-RAY DIFFRACTION	16	( CHAIN C AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	C	2003
33	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 7:107 )	D	7 - 107
34	X-RAY DIFFRACTION	18	( CHAIN D AND ( RESID 108:134 OR RESID 190:265 ) )	D	108 - 134
35	X-RAY DIFFRACTION	18	( CHAIN D AND ( RESID 108:134 OR RESID 190:265 ) )	D	190 - 265
36	X-RAY DIFFRACTION	19	( CHAIN D AND ( RESID 135:189 OR RESID 2002:2002 ) )	D	135 - 189
37	X-RAY DIFFRACTION	19	( CHAIN D AND ( RESID 135:189 OR RESID 2002:2002 ) )	D	2002
38	X-RAY DIFFRACTION	20	( CHAIN D AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	D	275 - 604
39	X-RAY DIFFRACTION	20	( CHAIN D AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	D	2001
40	X-RAY DIFFRACTION	20	( CHAIN D AND ( RESID 275:604 OR RESID 2001:2001 OR RESID 2003:2003 ) )	D	2003
41	X-RAY DIFFRACTION	21	( CHAIN E AND RESID 7:107 )	E	7 - 107
42	X-RAY DIFFRACTION	22	( CHAIN E AND ( RESID 108:134 OR RESID 190:265 ) )	E	108 - 134
43	X-RAY DIFFRACTION	22	( CHAIN E AND ( RESID 108:134 OR RESID 190:265 ) )	E	190 - 265
44	X-RAY DIFFRACTION	23	( CHAIN E AND ( RESID 135:189 OR RESID 2002:2002 ) )	E	135 - 189
45	X-RAY DIFFRACTION	23	( CHAIN E AND ( RESID 135:189 OR RESID 2002:2002 ) )	E	2002
46	X-RAY DIFFRACTION	24	( CHAIN E AND ( RESID 275:607 OR RESID 2001:2001 OR RESID 2003:2003 ) )	E	275 - 607
47	X-RAY DIFFRACTION	24	( CHAIN E AND ( RESID 275:607 OR RESID 2001:2001 OR RESID 2003:2003 ) )	E	2001
48	X-RAY DIFFRACTION	24	( CHAIN E AND ( RESID 275:607 OR RESID 2001:2001 OR RESID 2003:2003 ) )	E	2003
49	X-RAY DIFFRACTION	25	( CHAIN X AND RESID 2:11 )	X	2 - 11

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein / DNA chain , 2 types, 7 molecules ABCDEFX

-
Non-polymers , 5 types, 36 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein / DNA chain , 2 types, 7 molecules ABCDEFX

-Non-polymers , 5 types, 36 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein / DNA chain , 2 types, 7 molecules ABCDEFX

-
Non-polymers , 5 types, 36 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi