PDB-7qqu: SpCas9 bound to FANCF off-target2 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qqu

Title

SpCas9 bound to FANCF off-target2 DNA substrate

Components

(FANCF off-target2 ...) x 2
CRISPR-associated endonuclease Cas9/Csn1
FANCF sgRNA

Keywords

HYDROLASE / crispr / cas9 / off-target / ternary complex

Function / homology

Function and homology information

maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function

Biological species

Streptococcus pyogenes (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Pacesa, M. / Jinek, M.

Funding support

Switzerland, 1items

Citation

Journal: Cell / Year: 2022
Title: Structural basis for Cas9 off-target activity.
Authors: Pacesa, M. / Lin, C.H. / Clery, A. / Saha, A. / Arantes, P.R. / Bargsten, K. / Irby, M.J. / Allain, F.H. / Palermo, G. / Cameron, P. / Donohoue, P.D. / Jinek, M.

History

Deposition	Jan 10, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 26, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7qqu.cif.gz	841.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7qqu.ent.gz	568.1 KB	Display	PDB format
PDBx/mmJSON format	7qqu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7qqu_validation.pdf.gz	471.1 KB	Display	wwPDB validaton report
Full document	7qqu_full_validation.pdf.gz	487.8 KB	Display
Data in XML	7qqu_validation.xml.gz	55.6 KB	Display
Data in CIF	7qqu_validation.cif.gz	80.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqu ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqu	HTTPS FTP

-
Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqrC 7qqsC 7qqtC 7qqvC 7qqwC 7qqxC 7qqzC 7qr0C 7qr1C 7qr5C 7qr7C 7qr8C 7zo1C 5fq5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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 (16) #253 - Jan 2021 Expressome similarity (2) #121 - Jan 2010 70S Ribosomes similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #67 - Jul 2005 TATA-Binding Protein similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #227 - Nov 2018 Telomerase similarity (2) #122 - Feb 2010 Enhanceosome similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #135 - Mar 2011 Integrase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #65 - May 2005 Self-splicing RNA 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) #98 - Feb 2008 Small Interfering RNA similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #161 - May 2013 Ricin similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase 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 (16)
#253 - Jan 2021
Expressome
similarity (2)
#121 - Jan 2010
70S Ribosomes
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (2)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#227 - Nov 2018
Telomerase
similarity (2)
#122 - Feb 2010
Enhanceosome
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#65 - May 2005
Self-splicing RNA
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)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (2)

Deposited unit

A: FANCF sgRNA

B: CRISPR-associated endonuclease Cas9/Csn1

C: FANCF off-target2 target strand

D: FANCF off-target2 non-target strand

hetero molecules

199 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)	177.444, 67.492, 187.113
Angle α, β, γ (deg.)	90.000, 111.168, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

-
FANCF off-target2 ... , 2 types, 2 molecules CD

#3: DNA chain	FANCF off-target2 target strand Mass: 8646.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	FANCF off-target2 non-target strand Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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

#1: RNA chain	FANCF sgRNA Mass: 27068.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein	CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9 Mass: 158588.781 Da / Num. of mol.: 1 / Mutation: D10A, H840A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

#1: RNA chain

FANCF sgRNA

Mass: 27068.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#2: Protein

CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9

Mass: 158588.781 Da / Num. of mol.: 1 / Mutation: D10A, H840A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pyogenes (bacteria) / Gene: cas9, csn1, SPy_1046 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

-
Non-polymers , 3 types, 611 molecules

#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.45→46.05 Å / Num. obs: 76249 / % possible obs: 99.7 % / Redundancy: 6.6 % / B_iso Wilson estimate: 49.12 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.13 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2.45→2.54 Å / Redundancy: 6.3 % / R_merge(I) obs: 1.53 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7533 / CC_1/2: 0.451 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
Coot		model building
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FQ5

5fq5

Resolution: 2.45→47.81 Å / SU ML: 0.364 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2312	3807	4.99 %
R_work	0.2022	72420	-
obs	0.2037	76227	99.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 65.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→47.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10846	2553	15	596	14010

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	13895
X-RAY DIFFRACTION	f_angle_d	0.5619	19264
X-RAY DIFFRACTION	f_chiral_restr	0.0387	2197
X-RAY DIFFRACTION	f_plane_restr	0.0031	2021
X-RAY DIFFRACTION	f_dihedral_angle_d	17.4944	5632

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 (%)
2.45-2.48	0.3449	141	0.3377	2653	X-RAY DIFFRACTION	99.54
2.48-2.51	0.3425	131	0.3225	2647	X-RAY DIFFRACTION	99.07
2.51-2.55	0.3498	140	0.3111	2648	X-RAY DIFFRACTION	99.86
2.55-2.58	0.3158	143	0.309	2692	X-RAY DIFFRACTION	99.89
2.58-2.62	0.348	144	0.2997	2624	X-RAY DIFFRACTION	99.39
2.62-2.66	0.3596	138	0.2926	2640	X-RAY DIFFRACTION	99.61
2.66-2.71	0.3439	142	0.2869	2697	X-RAY DIFFRACTION	98.75
2.71-2.75	0.3162	139	0.2798	2629	X-RAY DIFFRACTION	99.75
2.75-2.8	0.3155	142	0.2803	2699	X-RAY DIFFRACTION	99.3
2.8-2.86	0.3104	134	0.2579	2622	X-RAY DIFFRACTION	99.6
2.86-2.92	0.2897	148	0.2604	2644	X-RAY DIFFRACTION	99.89
2.92-2.98	0.2531	131	0.25	2707	X-RAY DIFFRACTION	99.82
2.98-3.05	0.275	145	0.2592	2664	X-RAY DIFFRACTION	99.96
3.05-3.13	0.2779	141	0.2502	2663	X-RAY DIFFRACTION	99.89
3.13-3.21	0.3068	144	0.2341	2701	X-RAY DIFFRACTION	99.96
3.21-3.3	0.2686	137	0.2211	2639	X-RAY DIFFRACTION	99.89
3.3-3.41	0.2483	141	0.2086	2700	X-RAY DIFFRACTION	100
3.41-3.53	0.2335	143	0.2079	2717	X-RAY DIFFRACTION	100
3.53-3.67	0.2405	141	0.1942	2655	X-RAY DIFFRACTION	99.93
3.67-3.84	0.1895	137	0.1816	2690	X-RAY DIFFRACTION	99.89
3.84-4.04	0.1749	144	0.1686	2699	X-RAY DIFFRACTION	99.96
4.04-4.3	0.1892	138	0.1569	2706	X-RAY DIFFRACTION	99.89
4.3-4.63	0.1775	145	0.1488	2686	X-RAY DIFFRACTION	100
4.63-5.09	0.19	143	0.1483	2707	X-RAY DIFFRACTION	100
5.09-5.83	0.2239	142	0.1653	2728	X-RAY DIFFRACTION	99.79
5.83-7.34	0.1817	145	0.1808	2752	X-RAY DIFFRACTION	99.93
7.34-47.81	0.182	148	0.1694	2811	X-RAY DIFFRACTION	99.5

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	0.310969875755	-0.30448001583	0.456052360409	0.322115740752	0.0190125469928	0.568051951081	-0.1007648785	-0.0757341781098	0.136726223134	0.0109769598766	0.0879781728622	0.0600072163987	0.325226058804	-0.119992586642	-3.95654526888E-5	0.42054603721	-0.0805832290533	0.0485487290051	0.383390368211	-0.0765303244075	0.408810538548	-7.29384957212	6.87955613685	60.9596529353
2	0.0981562257044	-0.188421613704	-0.0318069085818	0.128501282882	0.014822168917	0.231487774318	0.212263691682	0.210459936356	0.266830499404	-0.0181992319673	0.171617590416	-0.107214081984	0.37480559966	0.322777901341	0.0602206452257	0.454635077407	0.0653359230556	-0.0606126563947	0.6297689313	-0.062366374317	0.332319577353	18.3263439275	-5.5711980926	13.2923265454
3	-0.00045122156965	0.00221481907564	0.00653505393677	0.0349887698152	0.021516385265	0.010866703929	0.356806549902	-0.0348115242065	0.337139895766	-0.211130930488	0.172724338216	0.0213890134517	-0.0620841108878	-0.195209923612	2.81485297977E-5	0.959182895373	0.196820006584	-0.210378710709	1.03599157388	-0.157651821852	0.949584993164	19.4282253741	-19.7624967094	3.14024097397
4	0.285728562795	0.212025663707	0.36543966201	0.111367648806	-0.0337640035189	0.601808232027	0.0175552444104	0.0564431398035	0.118365268348	-0.0156019005254	0.022302816451	0.0773277871065	-0.00941597138302	0.112021110506	1.44111830555E-5	0.287740318011	-0.0347190078525	-0.0208915284071	0.327780529135	0.0157330581898	0.367335508901	-0.98590089459	8.62820090985	28.9941357306
5	0.012228454917	-0.00430935456014	0.02347652589	0.000134742892712	-0.00343112007713	0.011071957819	0.194171404699	0.0636571870017	0.322332650012	0.0529652143278	-0.0494247430259	-0.114364553642	-0.354680575829	0.298423482762	0.000597129813657	0.95949791882	-0.0373307161097	0.116273924885	0.663288611718	0.242159791334	1.06101494741	-38.7738437209	17.1861365968	29.1869841965
6	0.0616587199831	-0.0726894072888	0.0184848430616	0.0749814381824	-0.00994650608171	0.00404241912157	0.113056470917	-0.0138537128612	-0.305607575388	-0.136281111864	0.00171202574737	0.145682719993	-0.829149119617	0.0775455899989	0.000353610437334	0.817914057932	-0.169482452573	0.0830975605926	0.918570940228	-0.0285202514832	0.528656552662	-39.9191676112	14.398434784	37.1448526324
7	0.706670574604	0.142174978799	-0.158835967725	-0.00166359967475	-0.0915468565201	0.740357624991	-0.00812065850516	0.087049144791	0.0313262881974	-0.0127352609425	0.00265320229297	0.043924948215	0.00471884331934	0.131383680478	4.60375482744E-5	0.243274956514	-0.0638472609231	0.00872069607361	0.224544537418	-0.0145195193659	0.2828636693	-1.09278485638	7.13088809172	31.1667302148
8	0.335814032046	-0.175454121199	0.447750344654	0.516056528956	-1.13606509382	0.792349059311	-0.109182141602	0.181638248863	0.00388757111745	0.183089500916	-0.038666891073	0.000268183425546	-0.283913695615	0.181621149365	-3.98325346314E-5	0.500822045583	-0.0146092422249	-0.0418206527525	0.467359347127	-0.0353332621531	0.344891992686	27.2384003282	-0.0996200117477	62.2861320714
9	0.0761813395606	-0.137000981793	0.111697379912	0.0531611451487	0.0380128213903	1.11025301224	0.0248883985255	-0.0262971091045	0.0305957380509	0.0753012498853	0.0203348500168	-0.00269912579905	-0.0125738799954	0.280063802639	-0.000396961357284	0.261335250356	-0.0503542835139	-0.0182905755441	0.273023226827	0.00734879769904	0.321700383253	11.811131361	6.74169099254	47.8613916597
10	0.290621380887	0.0310624791378	0.239576468945	0.338625186738	-0.0513385277141	0.634040212699	-0.0941692556997	0.0167756637817	-0.002450950029	0.122380220602	0.0821730158924	-0.0496285588157	-0.158412222311	-0.0146373947523	-2.4987911162E-6	0.352523368869	0.0192444515383	0.00379851107449	0.260916656744	-0.0149030965014	0.344410886701	-5.26423504445	18.3607318061	74.84958926
11	0.547326199373	-0.449146300272	0.0317531402823	0.344991971778	-0.153231780192	0.672370794302	0.0227649422591	-0.0516072353779	-0.0912997953205	0.0890569211264	-0.0324647011684	0.0083498339071	0.148645157749	0.090160371442	-3.05951620255E-6	0.417306010829	-0.024079470328	-0.0488126573458	0.338258092639	-0.0197095828239	0.438038457114	-10.7205048051	-11.9872556915	66.2812223249
12	0.71861168915	0.165909283896	-0.219787880604	0.226089348251	-0.0165622166013	0.940764149879	-0.0906624850445	0.115790922584	-0.0435438657218	0.000374892486456	0.074031664938	-0.0116121312217	0.347072200732	-0.205489684171	0.000294433748437	0.34984116202	-0.117127697696	0.0137475576711	0.198313494921	-0.03103458478	0.280870235972	-29.0569794218	-13.6247115305	39.999458496
13	0.120041747084	0.254724857409	-0.0745150532188	0.647818457253	-0.213121119535	0.0707711308363	-0.0931678488673	0.0426369397557	-0.163179156438	0.238982971569	-0.182082286013	-0.413429032444	-0.0461198936298	-0.314698608772	-0.0513882295973	1.01833175377	-0.363438490335	0.0840564194133	1.04062972018	-0.384091760679	0.677527479049	-15.7302709887	-21.5303757533	18.980381788
14	0.093015402895	-0.118664104769	0.0219238194147	0.1817015078	-0.142089391817	0.0461116080433	-0.0754572117623	-0.122016477495	-0.0787067273998	0.200196159921	0.11069221276	0.142911154835	0.229569211181	0.130911151529	-5.45514188715E-7	0.492409368933	-0.0835116126664	0.0465252139196	0.411558682309	-0.0334817531014	0.466335125126	-1.67893710836	1.63562081164	47.0648956412
15	0.0142329219017	0.0406701212073	0.0761391061935	0.0350566351392	0.0891026350082	0.0865782826851	-0.129844527191	0.110070033404	0.304702125012	0.103740918956	0.225948041412	0.139259166156	0.411949011389	-0.337377360873	6.37428983848E-5	0.604713572447	-0.090944832918	0.0677129525143	0.51715382393	0.0110149448474	0.476743333135	-14.5145107273	2.89383239715	77.7548894502
16	0.207677772981	0.136542587597	-0.118023592579	0.219044212379	-0.0605337243233	0.0527693697681	0.0796939818611	0.356039228044	-0.777549203882	0.0226030467964	0.168985580531	0.0753055628016	0.37263007636	-0.107722484056	0.00503901585472	0.600724272979	-0.0718841272908	-0.0161229704431	0.435808879737	-0.144520779403	0.63377724171	-11.0953821083	-14.3923629429	24.9517073348

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 34 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 39 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 40 through 69 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 70 through 74 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 75 through 82 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 163 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 164 through 315 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 316 through 551 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 552 through 750 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 751 through 953 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 954 through 1367 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -7 through -3 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -2 through 12 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 13 through 20 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid -3 through 7 )

-
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://pdbjlvh1.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

-
FANCF off-target2 ... , 2 types, 2 molecules CD

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

-
Non-polymers , 3 types, 611 molecules

-
Details

-
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

-FANCF off-target2 ... , 2 types, 2 molecules CD

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

-Non-polymers , 3 types, 611 molecules

-Details

-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

-
FANCF off-target2 ... , 2 types, 2 molecules CD

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

-
Non-polymers , 3 types, 611 molecules

-
Details

-
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