PDB-5b2q: Crystal structure of Francisella novicida Cas9 RHA in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 5b2q

Title

Crystal structure of Francisella novicida Cas9 RHA in complex with sgRNA and target DNA (TGG PAM)

Components

CRISPR-associated endonuclease Cas9
DNA (5'-D(*TP*GP*GP*TP*AP*TP*CP*GP*G)-3')
Guide RNA
Target DNA

Keywords

HYDROLASE/RNA/DNA / CRISPR-Cas9 / genome engineering / HYDROLASE-RNA-DNA complex

Function / homology

Function and homology information

defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function

Biological species

Francisella tularensis subsp. novicida U112 (bacteria)
synthetic construct (others)

Francisella tularensis subsp. novicida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Hirano, H. / Nishimasu, H. / Nakane, T. / Ishitani, R. / Nureki, O.

Citation

Journal: Cell / Year: 2016
Title: Structure and Engineering of Francisella novicida Cas9
Authors: Hirano, H. / Gootenberg, J.S. / Horii, T. / Abudayyeh, O.O. / Kimura, M. / Hsu, P.D. / Nakane, T. / Ishitani, R. / Hatada, I. / Zhang, F. / Nishimasu, H. / Nureki, O.

History

Deposition	Feb 1, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 9, 2016	Group: Database references
Revision 1.2	Oct 4, 2017	Group: Advisory / Data collection / Derived calculations Category: diffrn_detector / diffrn_source ...diffrn_detector / diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_value_order / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5b2q.cif.gz	799.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5b2q.ent.gz	635.9 KB	Display	PDB format
PDBx/mmJSON format	5b2q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5b2q_validation.pdf.gz	521.7 KB	Display	wwPDB validaton report
Full document	5b2q_full_validation.pdf.gz	552.5 KB	Display
Data in XML	5b2q_validation.xml.gz	65.8 KB	Display
Data in CIF	5b2q_validation.cif.gz	99.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/5b2q ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b2q	HTTPS FTP

-
Related structure data

Related structure data	5b2oC 5b2pC C: citing same article (ref.)
Similar structure data	5b2p-d 5b2o-d 4yuu-3 6oce-d 4yuu-2 5v36-2 10024 6v4x-d 21050 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	#181 - Jan 2015 Cascade and CRISPR similarity (4) #253 - Jan 2021 Expressome similarity (2) #121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #67 - Jul 2005 TATA-Binding Protein similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #87 - Mar 2007 Zinc Fingers similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #227 - Nov 2018 Telomerase similarity (2) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA 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) #23 - Nov 2001 DNA 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) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#181 - Jan 2015
Cascade and CRISPR
similarity (4)
#253 - Jan 2021
Expressome
similarity (2)
#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (2)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#227 - Nov 2018
Telomerase
similarity (2)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
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)
#23 - Nov 2001
DNA
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)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (2)

Deposited unit

A: CRISPR-associated endonuclease Cas9

B: Guide RNA

C: Target DNA

D: DNA (5'-D(*TP*GP*GP*TP*AP*TP*CP*GP*G)-3')

hetero molecules

236 kDa, 4 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)	81.562, 158.977, 96.738
Angle α, β, γ (deg.)	90.000, 106.880, 90.000
Int Tables number	4
Space group name H-M	P12₁1

-
DNA chain , 2 types, 2 molecules CD

#3: DNA chain	Target DNA Mass: 8993.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis Source: (synth.) Francisella tularensis subsp. novicida (bacteria)
#4: DNA chain	DNA (5'-D(TPGPGPTPAPTPCPGPG)-3') Mass: 2786.833 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. novicida* (bacteria)

-
Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein	CRISPR-associated endonuclease Cas9 Mass: 190946.422 Da / Num. of mol.: 1 / Mutation: N995A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. novicida U112 (bacteria) Strain: U112 / Gene: cas9, FTN_0757 / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 References: UniProt: A0Q5Y3, Hydrolases; Acting on ester bonds
#2: RNA chain	Guide RNA Mass: 30278.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) synthetic construct (others)

#1: Protein

CRISPR-associated endonuclease Cas9

Mass: 190946.422 Da / Num. of mol.: 1 / Mutation: N995A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Francisella tularensis subsp. novicida U112 (bacteria)
Strain: U112 / Gene: cas9, FTN_0757 / Plasmid: pE-SUMO / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2
References: UniProt: A0Q5Y3, Hydrolases; Acting on ester bonds

#2: RNA chain

Guide RNA

Mass: 30278.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) synthetic construct (others)

-
Non-polymers , 7 types, 1043 molecules

#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#9: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₂H₆O₂
#10: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#11: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 993 / 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: 2.58 Å³/Da / Density % sol: 52.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 9-11% PEG 3350, 0.2 M calcium acetate, 0.1 M sodium acetate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→46.29 Å / Num. obs: 254994 / % possible obs: 98.9 % / Redundancy: 7 % / Net I/σ(I): 20.3

-
Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	1.10_2155: ???	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.7→46.286 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.55

	R_factor	Num. reflection	% reflection
R_free	0.206	12762	5.01 %
R_work	0.1831	-	-
obs	0.1842	254945	98.88 %

Solvent computation

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

Displacement parameters

B_iso max: 147.59 Å² / B_iso mean: 48.8681 Å² / B_iso min: 13.86 Å²

Refinement step

Cycle: final / Resolution: 1.7→46.286 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11701	2771	128	993	15593
B_iso mean	-	-	49.29	40.82	-
Num. residues	-	-	-	-	1588

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15216
X-RAY DIFFRACTION	f_angle_d	0.996	21129
X-RAY DIFFRACTION	f_chiral_restr	0.056	2415
X-RAY DIFFRACTION	f_plane_restr	0.006	2232
X-RAY DIFFRACTION	f_dihedral_angle_d	16.943	8857

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7193	0.3404	428	0.3294	7955	8383	99
1.7193-1.7396	0.3489	410	0.3159	8076	8486	99
1.7396-1.7608	0.3177	430	0.299	8050	8480	99
1.7608-1.7831	0.287	431	0.2861	8033	8464	99
1.7831-1.8065	0.2795	421	0.2681	8106	8527	99
1.8065-1.8313	0.2641	427	0.264	7990	8417	99
1.8313-1.8574	0.2807	423	0.2472	8096	8519	99
1.8574-1.8852	0.2782	429	0.2462	7985	8414	99
1.8852-1.9146	0.2311	421	0.224	7972	8393	98
1.9146-1.946	0.2448	420	0.2202	7956	8376	97
1.946-1.9796	0.2281	425	0.2062	8045	8470	99
1.9796-2.0156	0.2355	421	0.2009	8101	8522	99
2.0156-2.0543	0.2404	424	0.2042	8096	8520	99
2.0543-2.0963	0.216	430	0.1921	8102	8532	99
2.0963-2.1418	0.2257	422	0.1926	8131	8553	99
2.1418-2.1917	0.2096	427	0.1787	8046	8473	99
2.1917-2.2465	0.2055	423	0.176	8074	8497	99
2.2465-2.3072	0.1988	422	0.1789	8043	8465	98
2.3072-2.3751	0.2057	419	0.179	7997	8416	98
2.3751-2.4518	0.2144	428	0.179	8111	8539	99
2.4518-2.5394	0.2155	427	0.1748	8132	8559	100
2.5394-2.641	0.2051	430	0.1784	8101	8531	99
2.641-2.7612	0.2348	427	0.1878	8100	8527	99
2.7612-2.9068	0.2034	434	0.1812	8159	8593	99
2.9068-3.0889	0.192	413	0.175	7956	8369	98
3.0889-3.3273	0.1871	428	0.1708	8158	8586	100
3.3273-3.662	0.2061	426	0.1695	8142	8568	100
3.662-4.1916	0.182	434	0.154	8140	8574	99
4.1916-5.2798	0.1679	428	0.1504	8098	8526	98
5.2798-46.3031	0.1851	434	0.1843	8232	8666	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	1.3623	-0.219	1.2183	0.5685	-0.1524	4.1167	-0.0516	-0.2336	0.181	0.1305	0.0636	-0.0508	-0.1347	-0.076	0.0481	0.1423	-0	0.0193	0.1418	-0.0646	0.1934	3.9441	2.4404	25.2416
2	1.6574	2.2008	-0.8829	1.7856	-1.0434	-0.1896	-0.1393	0.2893	-1.1175	-0.2974	0.0343	-0.0534	0.4619	-0.074	0.092	0.6853	-0.0862	0.015	0.3767	-0.1242	1.1641	-15.9766	-33.7957	0.1748
3	1.5476	-0.3982	1.3374	0.4061	-0.1695	1.926	0.0488	0.3286	0.065	0.0222	-0.0279	-0.0876	0.1532	0.5552	-0.0241	0.1781	0.0138	0.046	0.306	-0.0351	0.2153	27.0186	-8.307	22.6813
4	1.0317	0.403	0.3251	3.9994	1.4446	0.8527	-0.1037	-0.0989	-0.3829	0.6156	0.2762	0.2221	0.5489	0.1583	-0.1474	0.5449	0.0569	0.0338	0.3329	0.0059	0.4344	22.8719	-31.4135	28.0989
5	1.508	-0.6441	0.0332	1.2042	0.4111	1.3222	-0.0646	-0.2598	-0.2177	0.1817	0.1471	0.0393	0.3697	0.0342	-0.0701	0.3789	0.027	0.0001	0.313	0.0188	0.2309	18.0581	-19.9521	38.5635
6	1.9525	-0.9211	-0.1048	1.6797	-1.2865	1.5971	0.5185	-0.0593	-0.4536	-0.4267	-0.28	-0.0561	0.8416	0.7184	-0.2884	1.1658	0.0406	-0.073	1.0702	0.2913	0.8102	7.8485	-30.7765	65.1718
7	2.6064	0.0899	-0.2911	3.1877	-0.4212	2.6023	-0.0484	-0.9657	-0.3434	0.4034	-0.0241	-0.0053	0.3276	-0.2529	0.0454	0.3246	-0.0056	-0.0283	0.6209	0.0192	0.2085	9.5123	-9.1556	56.0308
8	1.2541	-0.3848	0.6527	0.6592	-0.2306	1.0305	-0.1251	-0.183	0.1355	0.0295	0.0555	0.0849	-0.2174	-0.2001	0.0464	0.232	0.0075	0.0304	0.1661	-0.0312	0.2644	-22.0779	11.955	11.6056
9	1.1935	-0.0187	0.2105	2.7767	-0.1504	2.1929	-0.1359	-0.5333	0.4067	1.1466	0.1406	0.2058	-0.6996	-0.2191	-0.0058	0.743	0.1676	0.036	0.3859	-0.1661	0.3398	-15.935	19.2445	35.9444
10	3.0051	-0.3688	1.0729	1.4396	0.0878	1.8178	0.1686	-0.6456	-0.096	0.1584	0.0279	0.1501	0.4534	0.1474	-0.3044	0.703	0.0847	0.0488	0.482	0.0418	0.5033	16.6456	-24.4346	37.1521
11	1.973	-0.7392	1.5996	0.6092	-0.4218	3.0589	0.0659	-0.0817	-0.1714	-0.0152	0.0359	0.1759	0.2639	-0.0133	-0.156	0.1954	-0.0023	0.0233	0.1654	-0.009	0.2246	2.5605	-9.9013	17.6563
12	2.143	-0.5938	0.6805	1.3274	-0.437	2.7918	0.0859	0.2206	-0.0806	-0.0665	-0.0501	0.1269	-0.0204	0.0436	0.0005	0.2004	-0.0131	-0.0018	0.1701	-0.0123	0.2287	-16.4515	3.1365	-2.5431
13	5.0471	-1.1316	0.8134	4.1089	-1.1262	3.64	0.0689	0.7773	0.1782	-0.6722	-0.0762	0.5025	-0.3131	0.0475	-0.0228	0.4131	0.0286	-0.1403	0.4174	-0.0573	0.3703	-34.0593	8.2659	-16.0582
14	1.6274	-0.6679	0.6051	0.585	-0.1286	1.0276	-0.0038	0.1246	0.0341	-0.0835	-0.0335	0.0901	-0.0432	0.0171	0.0423	0.205	-0.0171	-0.0009	0.1289	0.0146	0.2141	-15.6189	6.288	-0.0879
15	4.7821	0.0787	-3.411	0.0304	0.1055	3.3996	0.2705	-0.0536	0.9376	0.2544	-0.5725	-0.1997	-0.9066	0.1781	0.2492	0.3799	-0.1168	0.0008	0.3012	0.0276	0.4287	7.8229	13.4686	8.723
16	1.8133	-0.4646	-0.2241	0.1714	0.0215	1.3505	-0.1683	-0.1013	0.179	-0.0697	0.0311	-0.0251	-0.1173	0.1241	0.142	0.2136	-0.0082	-0.0006	0.1892	-0.039	0.2615	2.4198	6.9613	22.3619
17	8.1022	5.0358	-1.267	6.8191	-4.4801	5.9159	-0.0445	-0.4817	0.8153	0.7234	-0.0577	-0.2356	-0.7749	-0.4966	0.0723	0.235	0.0778	-0.0717	0.2835	-0.0783	0.2292	9.5214	7.9713	30.294
18	3.9768	-1.383	0.6211	0.7583	-0.0678	0.2843	-0.0094	0.5644	0.5734	-0.0152	-0.1435	-0.3061	-0.0381	0.4272	0.1322	0.1696	-0.0335	0.018	0.3927	0.0321	0.2832	25.462	0.4168	15.8895
19	3.2039	3.1994	-3.3968	4.0176	-3.2704	3.6436	-0.1279	0.9664	-0.6629	-1.1009	-0.2422	-0.7417	1.2163	0.539	0.3446	0.4126	0.1322	0.0788	0.6074	-0.1201	0.3412	27.3654	-14.4837	9.1201
20	3.8168	1.0866	0.1064	2.7463	-2.1651	2.3916	-0.0884	0.3245	0.6227	0.1017	-0.1406	-0.2228	-0.1003	0.3701	0.1967	0.1259	-0.0332	-0.0101	0.3542	0.0235	0.3181	25.2048	-0.3332	16.2347
21	5.667	-2.5277	-2.8624	5.6166	1.5065	2.4145	-0.4282	-0.0206	0.2054	0.6728	-0.0801	1.2526	-0.3005	-1.3348	0.3785	0.4071	0.2728	0.024	0.7108	-0.0599	0.5938	-27.5225	13.1993	28.0354
22	0.7748	-0.2532	0.2289	0.8271	0.0648	1.1142	-0.1154	-0.424	-0.4841	0.4434	0.1927	0.1588	0.2141	0.1252	-0.1598	0.4549	0.0919	0.0715	0.3446	0.1144	0.3255	10.0414	-20.5309	29.2929
23	4.4722	-1.1304	-0.9356	1.6235	0.6867	0.37	-0.2324	0.1043	0.7753	0.3095	0.2027	1.27	-0.7159	-1.244	0.1359	0.4495	0.3288	0.0467	0.8657	0.0016	0.8371	-28.6504	16.5521	27.1303

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 1 through 99 )	A	1 - 99
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 100 through 324 )	A	100 - 324
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 325 through 643 )	A	325 - 643
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 644 through 750 )	A	644 - 750
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 751 through 927 )	A	751 - 927
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 928 through 1065 )	A	928 - 1065
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1066 through 1176 )	A	0
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1177 through 1457 )	A	0
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1458 through 1622 )	A	0
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 10 )	B	1 - 10
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 11 through 20 )	B	11 - 20
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 21 through 30 )	B	21 - 30
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 31 through 40 )	B	31 - 40
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 41 through 55 )	B	41 - 55
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 56 through 60 )	B	56 - 60
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 61 through 65 )	B	61 - 65
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 66 through 70 )	B	66 - 70
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 71 through 80 )	B	71 - 80
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 81 through 85 )	B	81 - 85
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 86 through 94 )	B	86 - 94
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1 through 10 )	C	1 - 10
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 11 through 30 )	C	11 - 30
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 1 through 9 )	D	1 - 9

-
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

-
DNA chain , 2 types, 2 molecules CD

-
Protein / RNA chain , 2 types, 2 molecules AB

-
Non-polymers , 7 types, 1043 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

-DNA chain , 2 types, 2 molecules CD

-Protein / RNA chain , 2 types, 2 molecules AB

-Non-polymers , 7 types, 1043 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

-
DNA chain , 2 types, 2 molecules CD

-
Protein / RNA chain , 2 types, 2 molecules AB

-
Non-polymers , 7 types, 1043 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