PDB-7qqz: SpCas9 bound to FANCF off-target7 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qqz

Title

SpCas9 bound to FANCF off-target7 DNA substrate

Components

(FANCF off-target7 ...) 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: 2.25 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	7qqz.cif.gz	843.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7qqz.ent.gz	570.6 KB	Display	PDB format
PDBx/mmJSON format	7qqz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7qqz_validation.pdf.gz	477.4 KB	Display	wwPDB validaton report
Full document	7qqz_full_validation.pdf.gz	504.5 KB	Display
Data in XML	7qqz_validation.xml.gz	54.2 KB	Display
Data in CIF	7qqz_validation.cif.gz	78.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqz ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqz	HTTPS FTP

-
Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqrC 7qqsC 7qqtC 7qquC 7qqvC 7qqwC 7qqxC 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) #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 (16)
#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: FANCF sgRNA

B: CRISPR-associated endonuclease Cas9/Csn1

C: FANCF off-target7 target strand

D: FANCF off-target7 non-target strand

hetero molecules

198 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)	177.801, 66.686, 187.607
Angle α, β, γ (deg.)	90.000, 110.830, 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-target7 ... , 2 types, 2 molecules CD

#3: DNA chain	FANCF off-target7 target strand Mass: 8604.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	FANCF off-target7 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, 510 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.: 11 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 497 / 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: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.25→46.13 Å / Num. obs: 97227 / % possible obs: 99.2 % / Redundancy: 6.5 % / B_iso Wilson estimate: 54.92 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.25→2.33 Å / Redundancy: 7 % / R_merge(I) obs: 1.82 / Mean I/σ(I) obs: 1 / Num. unique obs: 9668 / CC_1/2: 0.484 / % possible all: 99.8

-
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: 2.25→47.67 Å / SU ML: 0.3569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2472	4857	5 %
R_work	0.217	92302	-
obs	0.2185	97159	99.16 %

Solvent computation

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

Displacement parameters

B_iso mean: 70.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→47.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10910	2529	13	497	13949

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	13932
X-RAY DIFFRACTION	f_angle_d	0.4973	19308
X-RAY DIFFRACTION	f_chiral_restr	0.0362	2201
X-RAY DIFFRACTION	f_plane_restr	0.0028	2034
X-RAY DIFFRACTION	f_dihedral_angle_d	17.501	5650

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 (%)
2.25-2.28	0.3782	161	0.3554	3056	X-RAY DIFFRACTION	99.38
2.28-2.3	0.3594	164	0.3326	3116	X-RAY DIFFRACTION	99.97
2.3-2.33	0.345	158	0.3319	3011	X-RAY DIFFRACTION	99.91
2.33-2.36	0.3389	165	0.3162	3108	X-RAY DIFFRACTION	99.97
2.36-2.39	0.3685	150	0.313	3112	X-RAY DIFFRACTION	99.94
2.39-2.42	0.3681	165	0.3143	3068	X-RAY DIFFRACTION	99.66
2.42-2.46	0.3577	168	0.3042	3050	X-RAY DIFFRACTION	99.94
2.46-2.5	0.3211	166	0.3018	3078	X-RAY DIFFRACTION	99.75
2.5-2.53	0.3369	158	0.2969	3072	X-RAY DIFFRACTION	99.94
2.53-2.58	0.3328	163	0.287	3108	X-RAY DIFFRACTION	99.85
2.58-2.62	0.3242	171	0.2912	3048	X-RAY DIFFRACTION	99.63
2.62-2.67	0.3228	162	0.2886	3053	X-RAY DIFFRACTION	99.01
2.67-2.72	0.3537	153	0.296	3070	X-RAY DIFFRACTION	99.35
2.72-2.77	0.366	157	0.3067	3094	X-RAY DIFFRACTION	99.36
2.77-2.83	0.3466	170	0.3044	3016	X-RAY DIFFRACTION	99.47
2.83-2.9	0.3514	166	0.2832	3126	X-RAY DIFFRACTION	99.34
2.9-2.97	0.3333	162	0.2906	3028	X-RAY DIFFRACTION	98.7
2.97-3.05	0.2998	161	0.2891	3060	X-RAY DIFFRACTION	98.56
3.05-3.14	0.3092	155	0.2863	2993	X-RAY DIFFRACTION	97.31
3.14-3.24	0.3235	152	0.276	2937	X-RAY DIFFRACTION	94.75
3.24-3.36	0.3156	154	0.2605	3082	X-RAY DIFFRACTION	99.45
3.36-3.5	0.2668	171	0.2432	3102	X-RAY DIFFRACTION	99.63
3.5-3.65	0.2592	162	0.2233	3101	X-RAY DIFFRACTION	99.79
3.65-3.85	0.2245	161	0.2052	3105	X-RAY DIFFRACTION	99.63
3.85-4.09	0.2007	165	0.1746	3081	X-RAY DIFFRACTION	99.45
4.09-4.4	0.1843	161	0.1655	3104	X-RAY DIFFRACTION	99.51
4.4-4.85	0.2024	164	0.1593	3123	X-RAY DIFFRACTION	99.34
4.85-5.55	0.1716	166	0.1551	3107	X-RAY DIFFRACTION	97.91
5.55-6.98	0.2049	157	0.1742	3044	X-RAY DIFFRACTION	96.94
6.98-47.67	0.1711	169	0.154	3249	X-RAY DIFFRACTION	99.45

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	0.235900368391	-0.37156440691	-0.361796051038	0.352594898862	0.681613282315	2.37766275059	-0.176113062642	0.0258311595303	-0.0326544384742	0.22341315796	0.0647476907415	0.0448742716476	0.950519002441	-0.25955257022	0.172325955503	0.66610257213	-0.107977212207	0.0779277874895	0.581267013189	-0.0415281379244	0.555180352045	-6.96869273871	6.93857805553	61.1865085342
2	1.33911321007	-0.678387349771	0.0222859928584	0.948302530505	-0.480319766453	0.86293196146	0.42665014493	0.621958017566	-0.217766068643	-0.188580459032	-0.09767235376	-0.258096064972	0.637823349517	0.145345570278	-0.368007644583	0.617392994118	0.0892416480835	-0.000848758911573	0.762150848333	-0.135972827149	0.554858728584	18.3944078748	-5.45459067688	13.331178074
3	4.70607927548	1.13112447261	2.53223162568	0.934214894741	1.16488265859	4.20531479998	0.426558803504	0.117620213677	0.0641859186301	-0.510986953319	-0.0979652498131	0.58078618977	0.209632014418	-0.821762840879	-0.189279318281	1.34124588514	0.139781050968	-0.252031558294	1.24929855486	-0.222250877969	1.12470072192	19.0867449947	-19.8506175555	3.55914253141
4	1.16615221675	0.677554819488	0.345647924461	0.521977441972	-0.185562313756	0.702749905194	0.0659138458764	0.102184522227	0.124991280577	-0.04712836418	-0.00501883996131	0.0576717974109	-0.0292489048542	0.0383903266563	-0.0364918740885	0.471775645083	-0.0636734260883	-0.0336847692519	0.472879655117	0.00482512920923	0.453207112495	-0.773906489617	8.73256547939	29.1162525462
5	0.006826299748	-0.076173383673	-0.0300160500336	0.763316380855	0.350672677297	0.161452217875	0.391392095523	0.281569110605	1.24963842	0.0318361018561	-0.128774322931	-0.155141410982	-2.18476557997	0.877344376462	-0.327070450142	1.36298380709	-0.16927621425	0.181353804807	0.944997528675	0.232210535414	1.38157917323	-38.6160439922	17.287892497	29.2619386794
6	3.43658093399	-0.417005219151	0.0466060659578	3.63135096955	0.652068921429	4.11626565491	0.504737102507	-0.304308066046	0.185548984865	-0.150072699941	0.0662225545308	-0.504365784305	-1.64518664629	1.12347022628	-0.607754082794	0.996996115515	-0.339065944784	0.179839590817	1.08513805879	-0.0228708748339	0.938054127687	-39.6434546977	14.5355088595	37.3070141627
7	0.685427180251	0.198259442214	0.00810979593147	0.251830098768	-0.14849684591	0.55356895295	0.0911316127996	0.00833032256577	-0.00615848060381	0.0520863893055	-0.0887963663004	-0.0474492603303	-0.0225105479722	0.146247284733	0.0122980466895	0.462732244188	-0.0519156535597	-0.0115800342685	0.417084867928	-0.0228526071485	0.449520917798	6.06530579765	6.47815225315	37.4121799791
8	0.890412484645	-0.111136243297	0.988339695744	0.436845475303	-0.624223508853	3.21868421485	-0.0738605438984	-0.0871490661319	0.0259455647028	0.214305107566	-0.106274505525	0.0740743527163	-0.22093253524	-0.152316261728	0.193918352065	0.633737823517	0.0404330984209	-0.00552689152453	0.586385021843	-0.0108616057109	0.652997186456	26.4609038349	-3.57823936515	56.5415406464
9	1.49754637257	-0.0603596057682	-0.292153138852	0.549547550808	0.342956230886	1.38622720773	0.0976361719678	-0.0772919387249	-0.127285686944	0.150554684382	-0.0112676079047	0.00773584808458	0.0872392731187	0.200356086357	-0.0730363565003	0.484138938331	-0.0435158075001	-0.0497136330936	0.497744379644	0.0522351255909	0.46318033462	16.2257849777	5.92257670621	37.581756004
10	1.24446552638	0.183562721278	-0.538298830898	1.02629034355	-0.766811499422	2.29421440442	-0.0937084742251	-0.000820074193351	0.0237625199694	0.0214904912101	0.0447655667368	-0.108358233551	-0.00220091694642	0.0618368466013	0.0381302676473	0.45744297383	-0.00266772075955	-0.0244599632509	0.368703624647	-0.0411460489432	0.483318458412	0.860234432341	18.9797988521	80.6058917265
11	0.319665394481	-0.0792908805485	0.200513214393	0.181628086563	-0.242928000875	0.439777121466	0.0766116998579	0.0115747222098	-0.134883742192	-0.00380749841195	-0.0327985162088	-0.0612327446744	0.186514018089	0.00129376526302	-0.0420582137072	0.56305746493	-0.0208781476023	0.0102427679047	0.562491717549	-0.0192970280113	0.637891289677	-10.0141414983	-6.05803056191	66.360653825
12	0.890744152514	0.198593512854	-0.457962766905	0.372402166994	-0.179355400369	1.34696590714	-0.0985649668185	0.0311756931097	-0.167525034906	-0.0139696613931	0.0559996088888	0.0318799884219	0.375925213147	-0.177569680459	0.030888735628	0.517030875515	-0.097865040815	0.00501654822758	0.444886513376	-0.0130667294533	0.519078701543	-29.1344548919	-11.8427236971	43.6687665429
13	5.08298651261	2.37894077473	0.840085568104	1.90439395142	1.91884669592	3.12070448725	0.170839969934	0.988135653727	-0.560260942185	-0.206592965846	-0.306849202711	0.565614031036	-0.172894914545	-1.3596709082	0.230806763553	1.11426533072	-0.420101080971	0.108957273242	1.96037258241	-0.504683154435	1.03424846668	-16.0999434417	-19.8136385742	18.4573524753
14	0.391389011518	-0.0972344503771	-0.115035147213	0.0337509634776	-0.0649025285287	0.1658420201	0.023134398895	-0.115155547151	-0.130356023623	-0.0202024321234	0.0172155608467	0.0922953961068	0.0763691784495	0.0835683781079	0.0365952465363	0.55295498772	-0.0570726854281	0.0523297749162	0.605779723572	0.00474438375568	0.530722028374	-1.34024159538	1.60458572282	47.2489563301
15	0.162188250714	-0.0438793047633	-0.0675742978269	0.152134884137	0.460743277116	2.68373836083	-0.137126823951	0.321545201763	-0.175592998369	-0.289393141799	0.14644327472	0.238023313529	0.461566407712	-0.255865490375	-0.148463975481	0.799908183121	-0.135160882909	0.0280967584317	0.6477533114	-0.0319697973623	0.614002697418	-14.3351111187	3.04072734721	78.2154260098
16	4.49440158764	-0.627486854678	-2.32466161174	4.4803045244	0.262301284535	4.69275971571	-0.145413160147	0.596873976701	-1.06672635784	-0.146140487958	-0.01068062132	-0.249200609597	1.04890929365	-0.0188423396748	-0.12113572273	0.697229596036	-0.118157373444	-0.0480071018568	0.637274966004	-0.148112970852	0.82925115327	-11.5426953194	-14.0814327952	23.3605873137

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 207 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 208 through 342 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 343 through 493 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 494 through 678 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 679 through 905 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 906 through 1366 )
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 -2 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://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-target7 ... , 2 types, 2 molecules CD

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

-
Non-polymers , 3 types, 510 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-target7 ... , 2 types, 2 molecules CD

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

-Non-polymers , 3 types, 510 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-target7 ... , 2 types, 2 molecules CD

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

-
Non-polymers , 3 types, 510 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