PDB-8qfb: Crystal structure of human MPP8 C-terminal region (residues 565-860)

ID or keywords:

Entry

Database: PDB / ID: 8qfb

Title

Crystal structure of human MPP8 C-terminal region (residues 565-860)

Components

M-phase phosphoprotein 8

Keywords

TRANSCRIPTION / Transcriptional regulation / epigenetic silencing / antiviral response / genome stability / histone H3 lysine 9 methylation (H3K9me3) / transposable element (TE) / long interspersed nuclear element-1 (LINE-1) / RNA-binding protein / Human silencing hub (HUSH) complex

Function / homology

Function and homology information

: / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / heterochromatin / methylated histone binding / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / histone reader activity / nucleosome / chromatin binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.04 Å

Authors

Prigozhin, D.M. / Modis, Y.

Funding support

United Kingdom, 2items

Citation

Journal: to be published
Title: Structure and methyl-lysine binding selectivity of the HUSH complex subunit MPP8
Authors: Nikolopoulos, N. / Oda, S. / Prigozhin, D.M. / Modis, Y.

History

Deposition	Sep 4, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8qfb.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb8qfb.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	8qfb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8qfb_validation.pdf.gz	511.9 KB	Display	wwPDB validaton report
Full document	8qfb_full_validation.pdf.gz	552.7 KB	Display
Data in XML	8qfb_validation.xml.gz	92.4 KB	Display
Data in CIF	8qfb_validation.cif.gz	115 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/8qfb ftp://data.pdbj.org/pub/pdb/validation_reports/qf/8qfb	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/1043 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (1)

Deposited unit

B: M-phase phosphoprotein 8

A: M-phase phosphoprotein 8

C: M-phase phosphoprotein 8

D: M-phase phosphoprotein 8

E: M-phase phosphoprotein 8

F: M-phase phosphoprotein 8

G: M-phase phosphoprotein 8

H: M-phase phosphoprotein 8

295 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: M-phase phosphoprotein 8

defined by author
Evidence: gel filtration, Some dimer observed by SEC under non-reducing conditions
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: M-phase phosphoprotein 8

defined by author
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: M-phase phosphoprotein 8

defined by author
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: M-phase phosphoprotein 8

defined by author
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: M-phase phosphoprotein 8

defined by author
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: M-phase phosphoprotein 8

defined by author
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: M-phase phosphoprotein 8

defined by author
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: M-phase phosphoprotein 8

defined by author
36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.556, 179.531, 228.076
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 567 through 570 or (resid 571...
d_2	ens_1	(chain "B" and (resid 567 through 571 or (resid 572...
d_3	ens_1	(chain "C" and (resid 567 through 574 or (resid 575...
d_4	ens_1	(chain "D" and (resid 567 through 570 or (resid 571...
d_5	ens_1	(chain "E" and (resid 567 through 570 or (resid 571...
d_6	ens_1	(chain "F" and (resid 567 through 570 or (resid 571...
d_7	ens_1	(chain "G" and (resid 567 through 570 or (resid 571...
d_8	ens_1	(chain "H" and (resid 567 through 570 or (resid 571...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	SER	SER	ASP	ASP	A	B	567 - 736	43 - 212
d_1	2	PHE	PHE	LEU	LEU	A	B	738 - 859	214 - 335
d_2	1	SER	SER	ASP	ASP	B	A	567 - 736	43 - 212
d_2	2	PHE	PHE	LEU	LEU	B	A	738 - 859	214 - 335
d_3	1	SER	SER	ASP	ASP	C	C	567 - 736	43 - 212
d_3	2	PHE	PHE	LEU	LEU	C	C	738 - 859	214 - 335
d_4	1	SER	SER	ASP	ASP	D	D	567 - 736	43 - 212
d_4	2	PHE	PHE	LEU	LEU	D	D	738 - 859	214 - 335
d_5	1	SER	SER	ASP	ASP	E	E	567 - 736	43 - 212
d_5	2	PHE	PHE	LEU	LEU	E	E	738 - 859	214 - 335
d_6	1	SER	SER	ASP	ASP	F	F	567 - 736	43 - 212
d_6	2	PHE	PHE	LEU	LEU	F	F	738 - 859	214 - 335
d_7	1	SER	SER	ASP	ASP	G	G	567 - 736	43 - 212
d_7	2	PHE	PHE	LEU	LEU	G	G	738 - 859	214 - 335
d_8	1	SER	SER	ASP	ASP	H	H	567 - 736	43 - 212
d_8	2	PHE	PHE	LEU	LEU	H	H	738 - 859	214 - 335

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.5616031734, -0.820683964369, -0.105260183616), (-0.827205498162, 0.559710119578, 0.0495544735884), (0.018246628122, 0.114901752248, -0.993209266918)	-58.2159356212, -29.4182918616, -57.7027656365
2	given	(0.220679673956, 0.694940414445, -0.684367081232), (0.700320035883, -0.601272369367, -0.384738073468), (-0.678861052678, -0.394372106274, -0.619369286412)	-74.0226329233, 63.4571676667, -68.6403352836
3	given	(-0.728614031889, 0.111755286267, 0.675745772111), (0.100870471692, -0.958332685321, 0.267251963857), (0.677456080108, 0.262886325692, 0.686981833303)	-68.8501489585, 62.5855964922, 17.8576271824
4	given	(0.251230573519, -0.492727391129, 0.833128391642), (0.420904530019, -0.719480199655, -0.552437886928), (0.871620660344, 0.489456801297, 0.0266357677958)	-2.78515912715, -0.00261453072001, 58.3895610614
5	given	(0.239730839278, -0.385357315948, -0.891082972424), (0.385067836621, -0.804820771699, 0.451648410427), (-0.891208104709, -0.451401444932, -0.04455165109)	-53.3385107876, 28.3039833151, -6.7005329827
6	given	(0.355571162758, 0.74983984647, 0.557951030881), (0.773209062547, -0.571365440042, 0.275116847033), (0.525087510621, 0.333589176341, -0.782944038625)	15.0232299813, -5.67510988419, -30.8653870574
7	given	(-0.827348390809, 0.181443301463, -0.531575929271), (0.0434265122956, -0.922892498018, -0.382601065253), (-0.560007837673, -0.339628864287, 0.755674173363)	-59.3963804022, -50.3821161492, -24.6895062515

#1: Protein	M-phase phosphoprotein 8 / Two hybrid-associated protein 3 with RanBPM / Twa3 Mass: 36920.055 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Human MPP8 residues 546-860 with N-terminal hexahistidine tag Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99549
Has protein modification	Y

#1: Protein

M-phase phosphoprotein 8 / Two hybrid-associated protein 3 with RanBPM / Twa3

Mass: 36920.055 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Human MPP8 residues 546-860 with N-terminal hexahistidine tag
Source: (gene. exp.)

Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99549

Has protein modification

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.56 Å³/Da / Density % sol: 65.4 % / Description: Prismatic, needles
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 12.5% (w/v) PEG 4000, 20% (v/v) 1,2,6-hexanetriol, 0.5 mM Morpheus II Oxometalate Mix, 0.1 M Morpheus II GlyGly/AMPD buffer mix pH 8. PH range: 7.4 - 9.8

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 19, 2016 / Details: torroidal mirror
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9282 Å / Relative weight: 1
Reflection	Resolution: 3→141.03 Å / Num. obs: 85128 / % possible obs: 100 % / Redundancy: 13.2 % / B_iso Wilson estimate: 100.74 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.081 / R_pim(I) all: 0.023 / R_rim(I) all: 0.085 / Net I/σ(I): 14.8
Reflection shell	Resolution: 3→3.08 Å / Redundancy: 11.2 % / R_merge(I) obs: 2.36 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6191 / CC_1/2: 0.744 / R_pim(I) all: 0.725 / R_rim(I) all: 2.47 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
xia2		data reduction
PHASER	1.2	phasing
Aimless	0.5.27	data scaling
Coot	0.9	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.04→93.54 Å / SU ML: 0.6377 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.0736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2947	4134	5.12 %
R_work	0.2555	76617	-
obs	0.2575	80751	98.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 130.53 Å²

Refinement step

Cycle: LAST / Resolution: 3.04→93.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17740	0	0	0	17740

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	18051
X-RAY DIFFRACTION	f_angle_d	0.8458	24559
X-RAY DIFFRACTION	f_chiral_restr	0.0455	2929
X-RAY DIFFRACTION	f_plane_restr	0.0069	3215
X-RAY DIFFRACTION	f_dihedral_angle_d	4.9964	2494

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	B	A	X-RAY DIFFRACTION	Torsion NCS	0.630153951603
ens_1	d_3	B	A	X-RAY DIFFRACTION	Torsion NCS	0.660615825346
ens_1	d_4	B	A	X-RAY DIFFRACTION	Torsion NCS	0.700909074283
ens_1	d_5	B	A	X-RAY DIFFRACTION	Torsion NCS	0.745901021617
ens_1	d_6	B	A	X-RAY DIFFRACTION	Torsion NCS	0.712602852852
ens_1	d_7	B	A	X-RAY DIFFRACTION	Torsion NCS	0.62493901332
ens_1	d_8	B	A	X-RAY DIFFRACTION	Torsion NCS	0.686325085697

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 (%)
3.04-3.07	0.5494	137	0.5126	2361	X-RAY DIFFRACTION	95.42
3.07-3.11	0.5408	142	0.5051	2488	X-RAY DIFFRACTION	95.64
3.11-3.15	0.5636	144	0.4885	2461	X-RAY DIFFRACTION	97.27
3.15-3.19	0.5506	132	0.4782	2446	X-RAY DIFFRACTION	96.45
3.19-3.23	0.4492	138	0.4364	2482	X-RAY DIFFRACTION	97.25
3.23-3.27	0.4689	131	0.4241	2507	X-RAY DIFFRACTION	97.81
3.27-3.32	0.4497	129	0.4089	2532	X-RAY DIFFRACTION	98.19
3.32-3.37	0.4125	129	0.388	2489	X-RAY DIFFRACTION	98.46
3.37-3.42	0.4388	162	0.3611	2549	X-RAY DIFFRACTION	98.98
3.42-3.48	0.4023	131	0.3473	2488	X-RAY DIFFRACTION	98.9
3.48-3.54	0.4077	149	0.355	2548	X-RAY DIFFRACTION	98.76
3.54-3.6	0.4146	126	0.3621	2513	X-RAY DIFFRACTION	98.69
3.6-3.67	0.3764	128	0.366	2572	X-RAY DIFFRACTION	99.05
3.67-3.75	0.4109	141	0.3462	2531	X-RAY DIFFRACTION	99.15
3.75-3.83	0.3779	143	0.317	2557	X-RAY DIFFRACTION	99.41
3.83-3.92	0.3236	130	0.2987	2555	X-RAY DIFFRACTION	99.67
3.92-4.02	0.3087	133	0.2841	2558	X-RAY DIFFRACTION	99.67
4.02-4.13	0.3356	140	0.2785	2564	X-RAY DIFFRACTION	99.38
4.13-4.25	0.2867	132	0.2502	2580	X-RAY DIFFRACTION	99.63
4.25-4.38	0.2892	129	0.2481	2579	X-RAY DIFFRACTION	99.63
4.38-4.54	0.264	128	0.2125	2568	X-RAY DIFFRACTION	99.56
4.54-4.72	0.2787	147	0.2076	2593	X-RAY DIFFRACTION	99.67
4.72-4.94	0.2521	143	0.2108	2568	X-RAY DIFFRACTION	99.89
4.94-5.2	0.2199	139	0.2063	2592	X-RAY DIFFRACTION	99.53
5.2-5.52	0.2503	140	0.2003	2580	X-RAY DIFFRACTION	99.82
5.52-5.95	0.264	139	0.2262	2628	X-RAY DIFFRACTION	99.86
5.95-6.55	0.3016	140	0.253	2628	X-RAY DIFFRACTION	99.96
6.55-7.5	0.2844	133	0.236	2644	X-RAY DIFFRACTION	99.96
7.5-9.44	0.2151	145	0.1947	2684	X-RAY DIFFRACTION	99.96
9.45-93.54	0.2099	154	0.1792	2772	X-RAY DIFFRACTION	98.99

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	4.34485720929	3.24443951718	0.622510642416	6.63860519012	-0.0247843706448	4.37549923523	0.0938115939983	0.124867160358	0.45493213461	-1.02919184566	-0.153214385423	2.23601489461	-0.515481670504	-1.47788346744	0.199958813221	0.954086384463	0.267197879116	-0.167638272518	1.22472272173	-0.190148634161	1.46705079411	-66.0345615139	5.81485199274	-49.4161407605
2	5.92262388429	-1.2181324054	0.749156764175	6.29789023254	-1.07564301458	4.07570722466	0.480372559927	0.48218094536	0.0665917333636	-0.927809290038	-0.714629313082	-0.521339892323	0.321115085553	0.167562293771	0.239677691196	0.982436652463	0.398275283701	0.245777133925	1.02785699246	-0.0669252379323	0.959292103001	-37.5507538076	7.45777463916	-47.152882082
3	3.09361073493	-1.03379537001	-0.917333755767	5.64432424568	-1.22240942358	6.32021275182	0.302499784689	0.208406714568	-0.723566547946	-0.818273321134	-0.65386545832	-0.099532185222	0.931987056584	0.746760770188	0.433797242478	1.2202722611	0.554221579572	0.345264435943	1.15937959945	0.0175187978625	0.963117649958	-29.6730873822	-8.79820965507	-46.2150277873
4	6.90066757545	2.58550079395	0.336673161835	9.00909952932	2.61559528182	4.28394712739	0.421766637036	-0.924763202032	-0.111861456067	-0.238204141947	-0.666926486489	-1.7547758422	-1.74934383879	0.269050477108	0.388626281981	0.839206363236	0.0472062830275	-0.153075240457	0.854538772665	0.166426155864	1.24804601613	-20.8951193352	34.1252572747	-5.27667927465
5	5.38582832494	2.40137580377	0.330683084021	7.6088307409	1.58150650731	0.586719767167	0.469430208805	0.122702271588	-0.197713447443	0.942106450604	-0.284982986271	-0.255844774024	0.0765074663644	0.128750410485	-0.195406632571	0.58023905291	0.19383499598	0.0914346361001	0.763624642356	0.0610826087787	0.628253366408	-36.7455088796	15.2798363132	-6.10729145779
6	7.54593213532	-0.711596555683	0.508254521309	8.68551631477	0.840547046237	4.230185101	-0.639757179339	0.0133222897163	-1.07049834942	-0.271440131737	0.334678313865	1.26052334918	0.200514862984	-0.376961757985	0.391157533757	0.814537975445	0.114176401416	0.186959420888	0.74121858431	-0.122438629649	0.77585670556	-42.8955164825	-4.81130684812	-16.9208522051
7	4.36168234244	-0.93878322773	0.139453056136	6.45292113033	0.500595972136	6.93272762398	-0.262475126793	-0.0649429152513	-0.768723559596	0.281802917457	0.0501906229109	-0.672363183718	1.10193212203	0.398847099754	0.148780687655	1.2544133779	0.378053306529	0.173857430451	0.763668474003	-0.022391142905	1.02623298811	-33.0524843195	-10.6873034331	-13.3328003891
8	6.40689224299	5.05114549305	-4.93779581729	4.28185567336	-4.2817583151	5.15189592051	-0.325027366412	1.90529192595	0.815604837956	-1.97312697625	-0.166823896212	-0.737818206457	1.39494781625	0.184288319703	0.362649178244	1.93742216088	0.904709830398	0.0856646431618	2.10490074311	-0.0255955101898	1.2520474122	-55.3397322618	30.5386730807	-61.7937833123
9	3.96848537569	-1.89733559879	-3.03558741018	5.95713316147	3.22020948858	4.46728572773	0.425471135228	0.892906607467	-0.998284866087	-0.425556693254	-0.724712065511	0.868166646675	-0.409843618127	-0.622031379627	0.155255095738	1.04692977357	0.560001791363	-0.0979674409405	1.26689078017	0.0516329167288	1.02548177404	-69.2090613409	32.8219639636	-39.4053042741
10	7.64000228952	-0.529141989477	-3.23746700869	3.6357984374	0.57148190568	5.42107941246	1.0336702379	-0.0197692902218	-1.76120588924	-0.0867742641706	-1.06295877743	0.286172724388	-0.839589626993	-0.111580379888	0.0877157664056	1.271662196	0.540581209104	0.144779233851	1.35821175885	0.339027705707	0.560180756513	-77.6516702233	48.1023004236	-30.2975836841
11	6.55193093468	0.243646224436	-1.17528056578	3.5794722349	3.61950047432	3.59948458987	0.701981847574	0.785089439407	-1.31904108632	-0.564716810115	-0.446293437588	1.15952367532	0.344435813346	-0.10846546288	-0.253642438971	1.30390671925	0.614173538559	0.109408470619	1.05488196278	0.0814974882533	1.37434859498	-83.6069902931	48.1184781397	-31.0796877517
12	5.40958913908	-0.578741234663	2.22861657265	6.79686355048	2.83756849686	4.35756225189	0.125700672141	0.852004481458	0.447181882043	-0.148985407294	0.00563602382348	0.815840931554	-0.72208712653	-0.122020654811	0.0163924859994	1.10390300444	0.516243748017	0.246151354975	1.13430841872	0.250039140616	0.89257716169	-78.1470592033	53.646004532	-34.6985461453
13	9.29829188056	2.7718247198	0.201988147793	2.81333781339	-2.47901673547	8.43752655997	0.720115022408	-0.4427861592	-0.0112340606344	1.36019612308	-0.450673428434	0.338011162617	-0.525118048019	-0.23146110472	-0.360573687501	0.873067284526	0.054737694531	0.176391636855	0.695679611893	0.0793675902672	0.733084067142	-51.8008622224	29.3509005999	7.28501846048
14	7.33908683639	0.552671004358	-0.610469962314	9.44884054483	-0.603032112023	6.74550034197	-0.0901642516277	0.330100445497	0.522352884252	0.719675996464	0.117892321168	0.370284921153	-1.05236716909	-0.623674805139	-0.0374749597619	0.530801599954	0.160531638645	0.0993219183452	0.661521974453	0.157183030918	0.541737389539	-49.4061883113	37.1599780545	-4.02603641132
15	4.62154374827	-0.582567940132	1.91044844806	6.40750596631	-0.215520875776	6.0941243299	-0.0161935883056	0.400512715455	0.654437066516	0.484574418245	-0.112960740748	-0.370560375976	-0.867653908935	0.58546009023	0.077994962344	0.591091839249	0.0965551180081	0.212083041696	0.730707390214	0.258550745185	0.858717538566	-42.9477483912	45.3641967688	-11.613143634
16	3.87079557643	-3.47017353706	0.43859677287	3.19796799725	-0.327832261457	4.05651101021	0.66448451787	1.22001282935	2.3559642196	-0.124665644044	-1.22195944407	-2.39732716449	-1.98653066099	1.66883594397	-1.04222503404	0.902478955192	0.20223876523	0.615907944567	1.29922595696	0.399708880353	0.991135804279	-37.2637362792	52.3357395944	-13.8053901986
17	3.42972931951	-3.56621582781	1.43568007203	5.47357824234	-0.217557655486	1.57447343653	0.996045219002	0.769271485058	1.41419080126	-1.8147837135	-0.934530871764	-0.534657359193	-0.0659024231407	0.358154876925	-0.0300397814268	1.02743789432	0.385219380352	0.391495648752	1.34195301725	0.58914897048	1.2466356034	-49.8998582429	58.4949951714	-24.2388213514
18	4.18938780936	3.87379258171	1.7339420294	4.83028544598	2.06100562025	3.40272112931	0.41081635927	0.685022035078	0.867925933525	0.269386285087	0.133372810292	-0.912529292853	-0.680595270094	-0.192648788909	-0.470093036366	1.29280298552	0.350914958337	0.179080081987	0.872743115594	0.359204861298	1.66836238012	-54.670698444	66.8012876152	-16.0875170913
19	4.76944071408	-0.575322084511	2.84491660502	9.86808982507	-1.06316334704	8.7040853163	0.779953867616	0.434565768515	1.1326013908	0.482073731362	-0.161010767137	0.753036541737	-0.178401680835	0.9152526389	-0.380434165386	0.626629507289	0.364323581157	0.351251204853	1.13075084684	0.436550895337	1.06770210935	-56.2799547491	61.5397603986	-18.4953334062
20	6.83059638795	0.777702063219	-0.519095922577	2.54458013482	2.69968303221	3.96978477966	0.54903931535	-1.73214983876	-0.031743302582	2.5469509119	-0.933040610128	-1.93803309699	1.14480157077	-0.208410505743	0.467626136572	2.10022630888	-0.549959227682	-0.85657017226	1.25025542009	0.488872514716	1.66907607345	-29.3985624178	-29.83874687	56.1773498368
21	3.98336505681	1.51557478319	-2.38485027252	4.06572829464	0.489028394774	9.03637569606	0.816831091518	-0.987426809686	0.0766727749785	0.847814409732	-0.971412133327	-1.95064624273	-0.193686758745	0.817661846523	-0.0742084127221	1.12577842196	-0.315332443443	-0.633773147381	1.13357208087	0.474905109679	1.80032198469	-25.7736931	-24.7140410476	45.071477714
22	3.15371318603	5.59723065724	-2.46613563244	8.65685874562	-3.92192312306	6.4392530549	-0.453678700969	0.122891639184	-1.4088116044	-0.936117571038	0.00543142573281	-1.34372086155	0.204869311048	-0.209061104992	0.315540539817	0.96770543849	-0.114117788118	-0.161725901495	0.78980885954	0.0723836598894	1.40919254674	-24.9372324872	-15.182321379	24.1422667951
23	7.70387976561	-0.731754098362	-1.3214269911	1.59416465341	-0.398324057205	3.75330951579	0.291927827776	0.171519354087	0.251281989687	0.0428245269975	-0.271380138577	-1.64221012024	-0.547674438564	0.353961311521	-0.0852104505088	1.0972574978	-0.388404229596	-0.0461883085595	0.978474517541	0.240373595193	1.43039524131	-17.2683461789	1.92062008785	23.3006108092
24	8.89979726353	-2.50628741573	6.28540444319	4.04354525153	-0.737238393409	5.54684997605	-0.124740226483	-0.348708660212	-0.550856934191	-0.0197339008121	-0.351467872693	-1.51432748759	-0.72346408258	0.313492377187	0.335010175317	1.11885891991	-0.203287825589	-0.0561804303911	0.717583587714	0.207064857385	1.34261184032	-16.2511459201	0.136970178117	24.9953557611
25	2.47425335912	1.58631858633	0.0474163983623	4.6364722912	0.00553214510423	4.31133680893	-0.63567248672	1.30847113298	-0.819625308517	-2.84735746109	1.13679014198	1.56406073542	-0.683986927757	-1.65648740317	0.220908506505	2.21109874154	-1.18293069833	-1.46493153658	1.14063551566	0.349042603412	1.78155747058	-66.6787053013	-7.08244050631	0.698672754578
26	2.32582338597	3.2376279742	0.761849974779	7.63770267397	-0.260282102131	4.58269355981	-0.295956089416	-0.185820811863	-0.0408304491741	-0.143403489297	0.0331867301562	1.26791938804	0.561620231716	-0.15232219327	0.233977847242	1.00892398165	-0.364970106648	-0.151060002742	0.970688053728	0.234991230071	0.871394773166	-56.406103566	2.35178178102	25.8011762361
27	6.32217237173	-2.62533891609	0.0234579687744	8.99311719131	0.368209625591	2.61112719538	0.303649628097	-0.674651417327	0.0409556152666	0.134962217935	-0.24320659186	0.642043327517	-0.749668159694	0.397976368782	0.0280905354164	1.11337115307	-0.417292039274	0.0574850894745	0.861683690165	0.0386978775481	0.650309805598	-45.23089023	18.0742694045	28.2353386305
28	5.65293589005	-6.29197499756	0.340210576046	2.02304815858	-3.01490785886	2.35497648197	-0.608568475207	-0.512896003397	0.667663155149	1.49096813071	0.599444169739	-4.05148735565	-0.633139402837	0.546691022011	-0.149534437098	0.71615743091	0.281747320434	-0.0141315150175	1.45454833143	-0.355515316026	4.01498898929	29.5056757751	-42.2060690818	-26.8740470421
29	7.09144119542	-1.73637949266	1.93135827739	7.37904972289	0.974241968424	3.88475775105	0.108408930287	0.714673306497	0.873520040112	-0.407473063657	-0.49480182062	-0.87967361654	-0.355346963644	-0.11147031284	0.37304959683	1.19250021356	0.247501195398	0.236988532622	0.784662753077	0.10009360977	1.04328105255	2.50170471915	-43.3326421962	-40.6734636203
30	7.27577164664	-1.09686984046	-0.281073492208	7.47176443447	-3.07192681401	6.73167300268	0.140988991351	0.607700431515	0.751001052622	-0.471997966526	-0.539278403806	-0.177575968323	0.0188607177793	-0.450894951823	0.346682740723	1.274349716	0.562241041843	0.160980337814	1.10781230813	-0.0549104598264	0.874847203199	-12.003940085	-28.8398310247	-41.4509742186
31	6.09527218552	2.68762130363	-0.744128512673	6.02204969512	2.06778094425	9.01839727901	1.13408169139	1.21470219637	-3.34123997222	0.00564309453924	0.423536328054	1.42911821937	0.292965333071	-1.1993597714	-1.53744968989	1.47542440761	0.377146029716	0.25250084651	1.34145684847	0.147449225247	2.75760878973	-33.2606740522	-79.5431199107	-28.0362941991
32	7.63746640606	2.20488052191	4.46181463039	3.10505086266	-2.07614495065	7.18110312478	0.669209344594	-2.24647510426	-0.208538341888	-0.33290151275	0.886681720676	1.28157370756	0.461846505165	-2.03329904755	-1.68405001926	1.15125938528	0.233020956346	0.343914708057	1.34193912019	0.340058946265	1.87781856105	-30.4148409194	-73.2632720018	-18.0559399579
33	2.15458952606	0.638419651009	1.4926567297	6.34420771947	0.435139989461	7.20069690291	-0.647406236802	-0.626953206889	-0.888343673833	0.396339171165	0.373287029617	1.99593072329	0.772002656093	-0.116306350127	0.26184821375	1.38823503431	0.571194541728	0.36267745905	1.08000068195	0.216793867893	1.71487252687	-24.4687917483	-67.5434181933	-20.5235622068
34	3.03018031175	-2.34871396753	1.29522327361	8.10067306574	1.48567781337	2.10303912688	-0.892062312418	-0.526626983055	0.0785029176836	2.18693388249	0.40653314191	0.47602975803	-0.3390807686	-0.120477868499	0.401897082078	1.84981220654	0.666508435593	0.385546477034	1.1983373192	0.173461080431	1.22391543581	-17.7568338964	-49.9720036357	-10.0535848565
35	4.43990469676	-0.0610836143564	-0.216872931396	3.13463500971	-0.817365119101	4.01896327423	-0.470087228064	-0.559610537018	0.393964939991	1.08740607019	0.0267451634303	0.734120712599	-0.753618140341	-0.364357066926	0.34762476105	2.04362462367	0.617132116836	0.330779680633	1.04654494212	-0.0247115900475	1.19103033615	-24.0324327715	-37.799441068	-12.3491089435
36	4.4305029957	-2.08632033418	-1.5182981984	5.65062535527	2.38310440222	1.14060449017	0.398763096293	-1.16565183171	1.52086450522	1.15822960483	0.674134654366	2.00118092559	-0.526172510827	-0.549074991727	0.820590717992	2.64806727857	1.15994023665	0.223561713773	1.18326140563	-0.22526791522	1.21536861864	-33.0805597746	-31.038070593	-15.3975535591
37	7.41861665577	1.97625641399	-0.772691062672	0.886161901872	-1.45394409722	5.57516555983	-1.69006284883	-0.878282131749	0.675973575415	1.24802488925	0.0078538753734	1.64034091702	-0.623849887637	-0.28324604698	0.824740704331	2.0726537069	0.949497832598	0.304896502084	0.804014724855	-0.0649141876629	1.10833180298	-27.7006721536	-38.0740044853	-12.2075213768

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 567 through 636 )	B	A	567 - 636	1 - 70
2	2	chain 'B' and (resid 637 through 760 )	B	A	637 - 760	71 - 194
3	3	chain 'B' and (resid 761 through 860 )	B	A	761 - 860	195 - 294
4	4	chain 'A' and (resid 563 through 596 )	A	B	563 - 596	1 - 34
5	5	chain 'A' and (resid 597 through 712 )	A	B	597 - 712	35 - 150
6	6	chain 'A' and (resid 713 through 760 )	A	B	713 - 760	151 - 198
7	7	chain 'A' and (resid 761 through 860 )	A	B	761 - 860	199 - 298
8	8	chain 'C' and (resid 567 through 613 )	C	C	567 - 613	1 - 47
9	9	chain 'C' and (resid 614 through 737 )	C	C	614 - 737	48 - 171
10	10	chain 'C' and (resid 738 through 760 )	C	C	738 - 760	172 - 194
11	11	chain 'C' and (resid 761 through 790 )	C	C	761 - 790	195 - 224
12	12	chain 'C' and (resid 791 through 860 )	C	C	791 - 860	225 - 294
13	13	chain 'D' and (resid 563 through 613 )	D	D	563 - 613	1 - 51
14	14	chain 'D' and (resid 614 through 656 )	D	D	614 - 656	52 - 94
15	15	chain 'D' and (resid 657 through 688 )	D	D	657 - 688	95 - 126
16	16	chain 'D' and (resid 689 through 712 )	D	D	689 - 712	127 - 150
17	17	chain 'D' and (resid 713 through 760 )	D	D	713 - 760	151 - 198
18	18	chain 'D' and (resid 761 through 840 )	D	D	761 - 840	199 - 278
19	19	chain 'D' and (resid 841 through 860 )	D	D	841 - 860	279 - 298
20	20	chain 'E' and (resid 565 through 597 )	E	E	565 - 597	1 - 33
21	21	chain 'E' and (resid 598 through 636 )	E	E	598 - 636	34 - 72
22	22	chain 'E' and (resid 637 through 760 )	E	E	637 - 760	73 - 196
23	23	chain 'E' and (resid 761 through 823 )	E	E	761 - 823	197 - 259
24	24	chain 'E' and (resid 824 through 860 )	E	E	824 - 860	260 - 296
25	25	chain 'F' and (resid 567 through 613 )	F	F	567 - 613	1 - 47
26	26	chain 'F' and (resid 614 through 760 )	F	F	614 - 760	48 - 194
27	27	chain 'F' and (resid 761 through 860 )	F	F	761 - 860	195 - 294
28	28	chain 'G' and (resid 565 through 597 )	G	G	565 - 597	1 - 33
29	29	chain 'G' and (resid 598 through 760 )	G	G	598 - 760	34 - 196
30	30	chain 'G' and (resid 761 through 859 )	G	G	761 - 859	197 - 295
31	31	chain 'H' and (resid 565 through 597 )	H	H	565 - 597	1 - 33
32	32	chain 'H' and (resid 598 through 613 )	H	H	598 - 613	34 - 49
33	33	chain 'H' and (resid 614 through 656 )	H	H	614 - 656	50 - 92
34	34	chain 'H' and (resid 657 through 760 )	H	H	657 - 760	93 - 196
35	35	chain 'H' and (resid 761 through 809 )	H	H	761 - 809	197 - 245
36	36	chain 'H' and (resid 810 through 823 )	H	H	810 - 823	246 - 259
37	37	chain 'H' and (resid 824 through 860 )	H	H	824 - 860	260 - 296

-
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

-
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

-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

-
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