[English] 日本語

Yorodumi

- PDB-8g0w: Crystal structure of human norovirus GII.4 P domain in complex wi... -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 8g0w

Title

Crystal structure of human norovirus GII.4 P domain in complex with Nanobody M4

Components

Nanobody M4
VP1

Keywords

VIRAL PROTEIN / Norovirus / nanobody / GII.4 / M4 / capsid

Function / homology

Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / VP1

Function and homology information

Biological species

Norovirus

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.87 Å

Authors

Hu, L. / Salmen, W. / Sankaran, B. / Prasad, B.V.V.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of human norovirus GII.4 P domain in complex with Nanobody M4
Authors: Hu, L. / Salmen, W. / Sankaran, B. / Prasad, B.V.V.

History

Deposition	Feb 1, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 4, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	8g0w.cif.gz	770.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8g0w.ent.gz	530.5 KB	Display	PDB format
PDBx/mmJSON format	8g0w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8g0w_validation.pdf.gz	488.9 KB	Display	wwPDB validaton report
Full document	8g0w_full_validation.pdf.gz	510.5 KB	Display
Data in XML	8g0w_validation.xml.gz	55 KB	Display
Data in CIF	8g0w_validation.cif.gz	74.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0w ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0w	HTTPS FTP

-
Related structure data

Related structure data	7jieS S: Starting model for refinement
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	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

-
Assembly

Deposited unit

A: VP1

B: VP1

C: Nanobody M4

D: Nanobody M4

E: VP1

F: VP1

G: Nanobody M4

H: Nanobody M4

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

A: VP1

B: VP1

C: Nanobody M4

D: Nanobody M4

defined by author
Evidence: gel filtration
95 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

E: VP1

F: VP1

G: Nanobody M4

H: Nanobody M4

defined by author
95 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.511, 90.675, 107.212
Angle α, β, γ (deg.)	90.000, 113.260, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

-
Components

#1: Protein	VP1 Mass: 34505.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: K4LM89
#2: Antibody	Nanobody M4 Mass: 13010.404 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.42 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 2% v/v Tacsimate TM pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16% w/v Polyethylene glycol 3,350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.87→48.82 Å / Num. obs: 41417 / % possible obs: 99 % / Redundancy: 3.7 % / B_iso Wilson estimate: 31.33 Å² / CC_1/2: 0.98 / R_merge(I) obs: 0.154 / R_pim(I) all: 0.106 / Net I/σ(I): 5.3
Reflection shell	Resolution: 2.87→2.99 Å / R_merge(I) obs: 0.468 / Mean I/σ(I) obs: 2 / Num. unique obs: 4625 / CC_1/2: 0.875 / R_pim(I) all: 0.33 / % possible all: 98.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PHENIX	1.20.1_4487	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7JIE

7jie

Resolution: 2.87→48.82 Å / SU ML: 0.4413 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.294	2006	4.85 %
R_work	0.2505	39338	-
obs	0.2526	41344	98.68 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.87→48.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12810	0	0	2	12812

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	13130
X-RAY DIFFRACTION	f_angle_d	0.5503	17897
X-RAY DIFFRACTION	f_chiral_restr	0.0416	1979
X-RAY DIFFRACTION	f_plane_restr	0.0047	2362
X-RAY DIFFRACTION	f_dihedral_angle_d	4.7823	1785

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 (%)
2.87-2.94	0.3888	139	0.3359	2767	X-RAY DIFFRACTION	98.14
2.94-3.02	0.3676	159	0.3241	2758	X-RAY DIFFRACTION	98.31
3.02-3.11	0.3729	134	0.3127	2786	X-RAY DIFFRACTION	98.28
3.11-3.21	0.3208	134	0.2903	2789	X-RAY DIFFRACTION	98.29
3.21-3.33	0.3848	149	0.2727	2794	X-RAY DIFFRACTION	98.53
3.33-3.46	0.3571	142	0.2692	2802	X-RAY DIFFRACTION	98.66
3.46-3.62	0.3168	158	0.2708	2764	X-RAY DIFFRACTION	98.72
3.62-3.81	0.2658	104	0.2424	2855	X-RAY DIFFRACTION	98.7
3.81-4.04	0.2987	141	0.2406	2789	X-RAY DIFFRACTION	98.45
4.04-4.36	0.2699	139	0.2136	2822	X-RAY DIFFRACTION	99.13
4.36-4.79	0.2114	175	0.1971	2798	X-RAY DIFFRACTION	98.94
4.79-5.49	0.2464	138	0.2051	2857	X-RAY DIFFRACTION	99.21
5.49-6.91	0.2897	151	0.2463	2838	X-RAY DIFFRACTION	99.2
6.91-48.82	0.2512	143	0.2425	2919	X-RAY DIFFRACTION	99.06

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	2.37110706253	-0.661026669216	0.113806853775	0.328926681497	-0.20193955268	0.231361078423	-0.0691631776977	0.149200525022	-0.308881891442	0.0252917716721	0.0962025132334	0.160058820446	0.103425834615	0.0888411749811	0.0439731046188	0.0965558368513	-0.0373472022285	0.0504360025407	0.181338609441	0.0410346233411	0.162215882733	6.06777806379	0.673831050331	10.7854228566
2	1.83127516484	-0.920870311524	-0.647410197067	2.26634352986	-1.14340216038	2.27512021271	-0.222332981748	-0.304075958727	-0.332016739653	-0.101487290124	0.00738003088426	-0.343580260268	0.256770790435	0.09080436459	0.155329552943	0.0942521599993	-0.00619641226846	0.0582831591482	0.258660420363	-0.0393180117092	0.233611342019	18.0668644109	-6.81638798272	14.4009050583
3	1.28094123647	-0.200851475521	-0.689752186704	1.21791561534	0.67626232367	1.84853859012	-0.00984256214374	-0.00109577054175	0.155040856229	-0.0218978695378	0.0212387007174	-0.120175999767	-0.306625079441	0.151401549777	0.0121970001056	0.108658301679	-0.0178138322148	0.00892659679504	0.139587184408	0.0316295385256	0.161067803471	-3.71095902756	14.7568999628	14.1531844168
4	0.87859503072	0.687778287505	-0.0173796269077	1.01449963217	-0.44905037455	0.910407651365	-0.130432337467	0.00663755640035	-0.138300330408	-0.132721025262	-0.00311027746999	0.0804750042755	0.306224998444	0.21383892055	0.130282967754	0.298221391742	0.101922575586	0.160122852138	0.169338823705	0.123016649332	0.251935708951	-10.1489512813	-14.74276216	18.5326147366
5	2.56746611946	0.903713818897	1.05205065712	1.19103472584	0.259197777251	1.55499904622	-0.0227972503486	-0.714082445784	0.123153016095	0.516681690641	-0.0339756965161	0.0663600734823	-0.128016721947	0.340745307664	0.0606958257249	0.376951100599	0.0635730089594	0.0201254674827	0.450231993959	0.0427601402524	0.183752527533	1.3270171042	-6.53462928927	34.8054653296
6	1.49274194632	0.139750991947	-1.30371814676	0.488781634708	-0.983780691014	2.69629064195	-0.0839584321154	-0.631413306011	0.20274220368	0.188698721705	-0.154677118403	-0.0375244851477	-0.585714018993	0.387505055522	0.0941029231158	0.519055077141	0.105937548158	-0.0992096657631	0.673848120314	0.0158838969075	0.210215932881	9.53020788853	-5.80383667377	37.2906438137
7	1.67054683425	0.911233162805	-0.526960054428	3.05000649159	-0.416928459446	2.55113013403	-0.106853859728	-0.6570340101	-0.324003589984	0.503920004473	0.0663704453987	-0.43283374736	-0.147414998018	0.794718650067	-0.188015167254	0.370670377943	0.150852195886	0.109802849509	0.571903275708	0.0436435821704	0.295869030776	10.5063284315	-11.5085091627	34.0030978259
8	2.15392277824	-0.13741312584	-0.0580263369134	1.0657442622	0.150951864643	0.383721121307	0.0085811019858	-0.235423301335	-0.371475081093	0.0161704848345	-0.10280128132	-0.166982768055	0.296376951298	0.104054653032	0.085633939929	0.200205343269	0.0291795693371	0.0904292600001	0.244468744733	0.108632510046	0.24499716178	-7.2864841973	-17.6348816378	25.2462928192
9	0.977237376338	0.160006132084	-0.503022350498	2.33731161367	0.166208263498	1.7467965479	-0.333237502538	0.174983664636	-0.497530323708	-0.323596427324	0.234757635103	-0.075215179329	0.931593474	0.00794699876439	0.0240178032273	0.528804777132	-0.0652384436711	0.107557979318	0.0720523429014	0.0190158528646	0.411601571604	-18.0519131212	-19.9812485245	10.2686560432
10	2.36094301703	0.174135881652	1.2355868282	4.84498378145	-0.674682011647	1.0385856688	0.0762549650249	0.0367843749097	0.0833973027385	-0.096713306469	0.0187019086181	-0.302498404546	-0.297932609209	-0.443249773848	-0.0906856228923	0.261119942683	-0.0651220385582	0.0146328609667	0.363959203531	0.200998018091	0.279395818701	-13.7221526969	5.15623914531	-13.4426874209
11	1.32882438945	-0.278331934156	0.376832389606	1.79327988114	0.29736708378	1.29137757103	0.139280833753	0.644830844073	-0.136663917952	-0.395427798474	0.0530425481712	0.18263926177	-0.146558706883	0.0325173579935	0.0896069062023	0.288216658203	-0.148654898269	-0.0551689033104	0.500942187475	-0.000450243605505	0.0868729017587	-6.53195869615	-2.42667993112	-19.7381035612
12	0.875440923107	0.542672351702	0.0238098438728	5.527315868	3.53069506277	2.3797896438	-0.196502525376	0.0651997282028	0.113887742122	-0.327996796432	0.514152697735	0.008169721288	-0.00521513097594	0.713637765379	-0.15288668061	0.506610483612	-0.10423116608	0.0127939137652	0.394494045062	-0.0519136849839	0.169778467929	-1.35443538289	0.223444996965	-22.6350940556
13	0.61696235831	-0.0167816911754	0.380536973011	1.20610122736	0.535855058269	3.77520661241	-0.312356164808	0.419163417581	-0.118049137921	-0.399127573763	0.0225615525288	0.235599727934	0.274375713869	0.0704891426387	-0.174655944869	0.254009227643	-0.0541571688828	-0.0435797355282	0.402147504145	0.0091794290845	0.159969343808	-10.43311009	-4.23265448293	-16.6159294199
14	3.51625357858	-4.1966963411	-3.8680541746	5.78156221553	3.7875427822	9.14309005574	-0.206726616799	0.529279337047	-0.0175098362912	0.0114866503548	-0.453168358297	0.649816075326	-0.422094469782	-0.0566246539094	0.422491572935	0.21348864205	-0.00730258179019	-0.0347140451788	0.338025872006	-0.0841235247376	0.329579187739	-34.5156826239	-2.15409641762	30.7229039205
15	0.0133275610203	0.00963972882234	0.00979526240741	0.00744931840966	0.00507225219583	0.012510306533	-0.00875245166138	0.0528360355447	0.133352308201	0.194336624184	-0.607609996555	0.230417174329	-0.596290533383	-0.290168622305	0.417208951867	0.803778827224	0.26561232076	0.02875734555	0.702807886838	-0.126495283624	0.636729823821	-46.1405934605	7.46893116952	49.4007717648
16	1.2242306954	-0.0849619391179	1.33905822564	3.84613538388	1.06559601766	1.80849422814	0.198204519106	-0.691989190269	0.0040197375738	0.412962623559	0.139732903828	0.0665145075691	0.0211029119822	-0.504161117913	-0.127540748764	0.254320650865	0.0529546262754	0.148785302777	0.303843168339	0.00921510178194	0.343831987672	-31.1684935397	-1.82651771578	37.8802084869
17	4.30429792332	1.19554826801	-1.58636347057	0.456252469546	0.353763004425	5.66642679383	-0.00977347037271	-0.538522670127	0.903304719278	0.204732515561	0.124222753924	0.195034200381	-1.0032963799	-0.100931050754	0.00244301925985	0.27526901898	0.00318075665085	-0.11848409602	0.28845142242	-0.062346296257	0.369108769163	-29.6477743328	10.1652099956	41.8971265959
18	4.26696991452	-1.1696581944	-3.30112581312	0.570460136059	1.72557757904	5.2948166569	-0.220171426253	-1.01556709098	-0.0794558715041	0.260212859472	0.293200203755	-0.00738463029785	0.168934795682	0.588751284423	0.127447329649	0.414666266895	0.0518972703111	-0.00366090111143	0.57097675113	0.00410872053608	0.269576581261	-23.5738628226	-1.8961183446	47.2457137433
19	0.995126318141	0.00802869218608	-0.566211283889	1.9001505493	0.630672458447	3.01966660748	-0.0296728828513	-0.559175391003	0.0933556127102	0.569419659971	-0.196398701481	0.172004907569	-0.0144842888092	0.21847397974	-0.193428928442	0.749903143252	0.102510012385	-0.0075833272203	0.609424498744	-0.128288520754	0.24937834917	-30.1707340078	8.05100785149	53.3396590854
20	3.17226325795	0.533373625356	-0.925405061991	0.378306186546	-0.700843542199	1.29830870589	-0.535710383939	-0.623998756106	-0.832061121491	0.331066965888	0.0428920381955	-0.0939801090927	0.400447968519	0.494262735413	0.191519130849	0.485362678649	-0.0121650746016	0.0386263104684	0.348151447436	0.170993544799	0.329330682731	-33.0289176805	-4.99073283749	44.3076663957
21	1.63326088405	0.826500794266	-0.369441157647	0.525186207208	0.0288210371217	0.520458736397	-0.118743599809	-0.631889991896	-0.168180526639	0.321190579548	-0.203441033809	0.0282311939139	0.618140792279	0.232550316884	0.269676209409	0.951092869158	0.334176398483	0.0858625204805	0.654328888909	-0.00130029168444	0.293049195031	-40.111290894	10.3871280226	51.1420454907
22	0.483397354435	0.655226956559	-0.230741009643	2.37678610608	-0.786835462302	1.17527961647	-0.0727669844434	-0.193332431086	0.437862877893	0.411098105071	0.0723008660768	0.0765214379909	-0.233580191323	0.325836300597	-0.0167843577007	0.203727646421	-0.0109813887823	-0.0189792306238	0.30770087527	0.0217919745314	0.205567810249	-25.0815503779	2.91911931375	32.2494646582
23	0.142083349692	-0.133126284256	0.0856354221138	0.125142297756	-0.111436994065	0.751436108887	0.0771856254747	-0.191445939736	0.358644522386	-0.226250116019	0.222211492053	0.206054699307	-0.217408378425	0.0306492688204	0.108642019616	0.123481576797	0.0164207384204	0.0132561373162	0.191570664235	-0.0294133086731	0.405914367795	-32.6601507546	4.40500686764	32.3523302168
24	0.874596214454	0.0152107479315	0.173923276035	0.418214002016	0.151293196112	0.231272328606	-0.00257605734441	0.0983889697296	0.0913080582859	-0.0172102028111	0.124234778468	0.225239656186	-0.178393574012	-0.0215163664194	0.161408357865	0.16708319312	-0.0894555372188	0.0627897255721	0.0297336618138	0.104851219003	0.129953744751	47.4026893986	-23.9103619505	-19.3567715491
25	1.57125221916	0.0368268925	0.230880990193	0.518266832262	0.0129429223675	0.673810949025	-0.0488980065473	-0.0441433443422	0.133051618628	0.126906838345	0.15959540203	-0.062673618641	-0.0319358616626	0.250737854948	0.114459414336	-0.0103825082643	0.0789676613272	-0.016542924626	0.158311888015	0.075640742625	0.158271543294	57.1362984355	-22.7493241811	-10.3330875657
26	2.27238827653	0.719433864316	0.211872133829	1.36816495489	-0.664451925437	0.748052320509	0.0072997864434	-0.14862428196	0.279753257624	0.172432521476	-0.00202444015734	-0.0218146045322	-0.0799706166634	0.0917041567256	0.0549966317468	0.131587345861	0.0182255637687	-0.113346747586	0.259615455861	-0.142856838404	0.202659254031	67.6666500061	-12.2025771417	-8.94764988563
27	2.54673613377	0.320708312028	0.231723801996	3.2627836577	-0.200798275914	1.46001953746	-0.192858343188	0.0727095009397	0.742239460164	0.124349646951	0.169103853686	0.112162418654	-0.164253175737	0.203561341236	0.206937680781	0.146970015599	-0.0876980965415	-0.10510816153	0.389594938644	-0.053649105244	0.333932996964	69.5947283738	-1.95469945751	-18.0964796199
28	2.64198600281	0.677995405108	0.359353993858	0.872193151837	-0.704185611208	1.16804834837	-0.243480050787	0.248428030893	0.269381903709	-0.0673856545629	0.0788723180297	-0.130040648316	-0.308884445957	0.219043502136	0.0736304942504	0.211049911592	-0.0322405827463	0.0126029282173	0.20526625836	-0.0610991066751	0.225419692082	70.6090845256	-13.8114386854	-12.9706840321
29	0.836030412592	0.484611199183	0.330828584664	2.60867075097	0.497831137968	1.44120929443	0.177146602135	0.102645465364	-0.0508084905438	0.160101357129	-0.0607198845093	-0.304199490376	0.274328557764	0.298556616955	0.147183921048	0.185105444634	-0.0359167959114	0.00694961499007	0.170892392324	0.0506287798918	0.00484712758526	57.1175524096	-32.7944427284	-7.96925082133
30	1.22288426583	0.415858153241	0.488833198515	1.93210098286	0.613169839342	1.1601553206	-0.145654543286	0.149916909041	0.115543753118	-0.25963447269	0.150818857845	-0.120150859416	0.114241662613	0.0264175930667	0.0545222570591	0.18158545164	0.00703542863148	-0.0185206846448	0.200191262066	0.0281594587722	0.0901268812969	47.0961111238	-27.9132163025	-16.3936200134
31	0.610404330237	0.358544352751	0.326334651983	1.19005943098	-0.442131981546	1.12831276365	-0.130001072861	0.112652660647	-0.121264076205	-0.168580576351	0.0709994559119	-0.230194049573	0.218698486479	0.131789465908	-0.113219554205	0.097910645053	0.0104927677848	0.00626702549613	0.183010599622	0.00693899279276	0.185643132234	46.0311531873	-37.7281199076	-18.1829713974
32	2.10658224212	-0.328210981961	-0.0653393560338	1.47831622967	0.659687104386	0.660162922851	-0.06702204946	-0.0620749781363	-0.56732531413	0.234916033184	0.0689718190097	0.0856839543656	0.181552490373	0.0280893767736	0.698569540013	0.0953917320219	-0.0113195108291	0.165737855684	0.126534960406	0.0745294037253	0.415794809892	38.4467278877	-39.1047783365	-12.5917814984
33	1.74474454994	-0.0117265614488	0.107401472206	0.863712209939	-0.605650148396	1.43124895341	0.0520082298117	0.196280644306	0.178067434813	0.136632014876	0.0427217280276	0.11235202743	-0.271288693122	0.0382914846985	0.19876399203	0.216860299793	-0.00123399027426	-0.145513323609	0.201091941781	0.0579870325649	0.146567440729	41.5958827984	-3.48810908388	-18.5139969761
34	1.10004608443	0.259950267954	-0.650998379971	0.935786462795	0.465901630797	2.15455344517	-0.0505044212138	0.0616110924608	-0.354365585181	0.0454515355541	-0.069503886234	-0.00575877295785	0.0222764282058	0.611522705247	0.0202103360811	0.191781588735	0.0166274712518	-0.0973080978103	0.329163482832	0.0953301418259	0.184627294738	48.4139187221	-13.0678193495	-30.4716966058
35	1.00569596735	0.0064963730411	0.398220562718	1.01369672016	0.716001326795	1.97838679917	-0.0192450825234	0.11782626265	-0.0297148756653	-0.171780585001	-0.0712946927535	-0.0376329656574	0.0381070635361	-0.056153382947	0.0493691495477	0.68919923463	0.0282969966917	0.207598185425	0.735128364579	0.000167783943568	0.18865660673	55.2640179278	-13.4647292164	-41.5826304575
36	1.69653742987	0.0501486457985	0.541797199731	0.698846593874	-0.892209529031	3.5093076565	0.0119440244109	0.520173151115	-0.0259084138961	-0.256897830513	-0.102624565384	-0.151132543665	0.336367556562	0.66052749345	0.114060820277	0.260423302002	-0.0115327553983	0.1433036503	0.590686550574	0.0987247311603	0.227025394376	58.5851651294	-10.6219805983	-35.1659778241
37	0.852955020517	0.356178843046	0.447422521361	2.74861986239	0.548562336011	1.72034247189	-0.211255469939	0.581566595543	0.174156781151	-0.320114016354	0.139392149526	-0.535615514101	0.0276117637543	0.599701385357	0.115319818727	0.333917714283	-0.0837232119837	-0.0212543507941	0.685661369142	0.202185312223	0.337878870026	63.4713464311	-6.6767456789	-34.4259476807
38	3.76736468032	-0.109298368744	-1.65947624984	1.09330063448	0.0950973500867	0.745795503789	-0.152276818943	0.784601076849	0.156022283275	-0.0683120864045	-0.100235332819	-0.133828764798	-0.110731321317	0.103321079241	-0.0656978469885	0.232222409393	-0.175997494858	-0.0346997929312	0.376460873801	0.180066022887	0.233799994768	44.3171726561	-0.0893573422978	-37.9644963372
39	1.27134594213	-0.442667735612	0.295045021931	0.61751783738	-0.236625110365	0.75565967102	-0.25271161811	-0.0516225531162	0.663531133774	0.409748294762	0.0186435732096	-0.0416039703871	-0.517986615316	0.0726663812408	-0.0618060122246	0.373112877246	-0.044027547638	-0.0975025128418	0.097438121109	0.0954263764575	0.293518673937	40.1205883914	0.554666294244	-14.9752423735
40	1.38600511656	-0.520572205541	-0.367597802567	0.330590190559	0.289399080762	0.269301123437	-0.119881997056	0.0103417646446	0.528797065893	-0.00149743231815	0.138701656753	0.201957565896	-0.659045900454	-0.0249378166906	0.019899838875	0.471856855122	0.0549994090656	0.00350459638911	0.0831286361679	-0.0349948253704	0.496922993437	28.6551304803	1.93372958299	-10.4095192806
41	0.996324866012	0.282225955579	0.171101794837	0.777026089013	-0.315840803547	2.45238389609	-0.00732241069251	-0.478655325306	0.181586223835	0.318819025377	0.0307662038244	0.0936160348967	-0.0676635511934	0.270584817532	-0.00821744192015	0.270063077961	0.112891529068	0.0297309359166	0.426976375237	-0.014391997966	0.201871680502	45.1226936783	-15.8931868522	19.665267553
42	1.7554190688	-0.370836404335	0.881563992545	1.27158212257	0.714573573833	3.77656221753	-0.159942134458	-0.25383005352	0.236330817044	0.754438606369	0.380267731727	-0.338611453365	0.627190747787	0.129026321324	-0.146047555852	0.354903257439	0.0688933474646	-0.00540108116866	0.562332536721	0.0884283022681	0.222738836434	48.0953996153	-18.4312067165	24.7197931277
43	0.053103825016	0.0959211293459	-0.201706157151	0.739959572568	0.632718725647	2.53144958464	-0.0961697945993	-0.313081745391	-0.0362025670778	0.188513153688	-0.0982136485297	-0.0125156088272	-0.193643090482	-0.172009418696	0.176828430373	0.129306050084	-0.00231039182266	-0.0660497900342	0.377170354686	-0.0296367684363	0.168550178368	40.4899391865	-15.0741740686	13.0110506448
44	6.12079263077	0.863535916529	-1.51918545459	3.0420742886	-0.0938280661227	0.405078754202	-0.230669207305	-0.679697902629	0.17874780627	-0.125509413615	-0.419306563361	0.165338226988	0.319521895661	-0.0365091487836	0.234648361569	0.32314414649	0.0458239285882	0.0403247572914	0.183210639856	-0.0266281739851	0.37253433757	17.2775829841	-15.9770528251	-30.7114573953
45	0.636993525262	0.32390959448	0.011826255676	0.620682689382	-0.00749144357491	0.000465635554856	-0.006286073401	0.0606654385109	-0.0282160641913	-0.0642519296401	0.103867048667	0.0342878348514	0.00720224775999	0.128620153549	0.204537855387	0.814062151842	-0.185234740939	-0.498460303877	1.08322617966	-0.050268319244	0.82209760973	5.22793789907	-25.1436867296	-49.428975077
46	0.741391582801	0.284479461864	-0.793576786067	0.58872769888	0.692026549039	2.89051198873	-0.142704708309	0.289892156784	0.408533708923	-0.449601748314	0.208963912414	0.323501706796	-0.148940619946	-0.680439741654	-0.369008841888	0.247065015352	-0.0639976168438	-0.0848004545734	0.273197600577	0.21054753995	0.420040341019	20.3307931066	-12.1476040977	-36.1827519332
47	2.16016616732	0.186902782573	-2.06006520896	2.70444966526	-1.18895200074	4.74418496481	-0.589195147887	0.0379125710348	-0.0871465306201	-0.153011851023	-0.117194795515	-0.0883589175819	0.471256503641	-0.241432969073	-0.137015302309	0.252344571117	0.0283629660117	-0.0112602443409	0.359806676947	-0.132646604907	0.354711957816	19.9966452841	-28.3380760773	-40.4441838139
48	1.93454168106	-0.438494842779	-0.847932556812	3.25615884461	-0.640998958451	1.76322326432	-0.206372015247	0.214042063516	-0.322020876101	-1.09371560892	-0.343364517877	0.195955142543	0.163010707333	-0.26841488647	0.429531423825	0.46254604703	-0.0261410402977	0.00405323953672	0.303339926195	-0.00427911919174	0.176841349064	25.9020483601	-20.4100994707	-44.7743487548
49	0.56913416032	0.605304558327	-0.690744681965	3.22743363002	0.963545236657	2.5618114339	-0.297311891113	0.556295082058	0.500980676673	-0.302653792627	0.260148579634	-0.0391796687983	0.358763374812	-0.195204265255	0.09253426944	0.510899240963	-0.0912062452291	-0.111297623406	0.450023582956	0.0705650341083	0.387237954708	20.858645912	-20.453905208	-49.9679136797
50	0.840000859821	-0.365444454184	0.400793903393	0.938528124002	-0.788116188756	1.58413768525	0.139396331067	0.0465702209955	-0.189206358187	-0.268977567669	0.136756209376	0.305915084234	0.136455159996	-0.380016669745	1.15762820777	0.517350849015	-0.00224279424273	-0.25341330021	0.413123171309	0.197316663764	0.410207402063	17.6857462447	-12.1874484576	-42.6412883549
51	1.34609431188	-2.42735390189	0.134823143861	4.38796084728	-0.28959676553	0.258037826366	-0.0113493392856	0.324552344497	0.171233073623	-0.690492642893	-0.245991747662	0.0521993995267	-0.00756812103272	0.195006849723	0.132420480307	0.519871641907	-0.292003802254	-0.240930469333	0.560214907284	0.235174294354	0.616426000019	11.7052352788	-28.6388450352	-51.0305880591
52	1.40812527371	0.448620583214	0.743659076499	0.873217694981	0.875251795171	0.950674104554	0.0337845449447	-0.00417897569904	0.0955435499358	-0.0470787878253	0.103810157709	0.193999609453	0.315587515738	-0.503360348772	0.223904869786	0.228382463296	-0.0271870869585	-0.172777927353	0.352944571341	-0.00617527234084	0.182010444434	20.0350584485	-22.9390348651	-37.0463055673
53	4.77369219105	0.272553487851	-2.90039718037	1.4061793619	-0.902675416359	4.05441665956	-0.268414981194	0.292368688056	-0.615350713913	-0.108892425378	-0.0498282257787	-0.0568933625064	0.293034741663	-0.218966398075	-0.10409944082	0.0921183585562	0.00472606467409	-0.0262384201793	0.121357931879	0.0439267728013	0.224558750119	32.0896164338	-19.6554224715	-28.2199627351
54	1.69028649542	0.418487699489	-0.187149661564	1.3242071369	-1.36165912834	2.23754200782	0.226002643182	0.273425752187	0.0538203876309	-0.426564947157	0.206696732249	-0.155718202727	0.290807868122	-0.300509596278	0.218622733437	0.281871470759	-0.0542327695506	-0.0637776442375	0.335902044436	-0.160099277583	0.28412624605	17.7888730379	-23.1485830029	-33.488612259

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 'A' and (resid 226 through 323 )	A	A	226 - 323	1 - 98
2	2	chain 'A' and (resid 324 through 408 )	A	A	324 - 408	99 - 173
3	3	chain 'A' and (resid 409 through 531 )	A	A	409 - 531	174 - 296
4	4	chain 'B' and (resid 222 through 267 )	B	B	222 - 267	1 - 46
5	5	chain 'B' and (resid 268 through 338 )	B	B	268 - 338	47 - 111
6	6	chain 'B' and (resid 339 through 363 )	B	B	339 - 363	112 - 136
7	7	chain 'B' and (resid 364 through 403 )	B	B	364 - 403	137 - 171
8	8	chain 'B' and (resid 404 through 464 )	B	B	404 - 464	172 - 231
9	9	chain 'B' and (resid 465 through 531 )	B	B	465 - 531	232 - 298
10	10	chain 'C' and (resid 1 through 7 )	C	C	1 - 7	1 - 7
11	11	chain 'C' and (resid 8 through 59 )	C	C	8 - 59	8 - 59
12	12	chain 'C' and (resid 60 through 82 )	C	C	60 - 82	60 - 82
13	13	chain 'C' and (resid 83 through 117 )	C	C	83 - 117	83 - 117
14	14	chain 'D' and (resid 1 through 7 )	D	D	1 - 7	1 - 7
15	15	chain 'D' and (resid 8 through 17 )	D	D	8 - 17	8 - 17
16	16	chain 'D' and (resid 18 through 39 )	D	D	18 - 39	18 - 39
17	17	chain 'D' and (resid 40 through 52 )	D	D	40 - 52	40 - 52
18	18	chain 'D' and (resid 53 through 59 )	D	D	53 - 59	53 - 59
19	19	chain 'D' and (resid 60 through 66 )	D	D	60 - 66	60 - 66
20	20	chain 'D' and (resid 67 through 82 )	D	D	67 - 82	67 - 82
21	21	chain 'D' and (resid 83 through 91 )	D	D	83 - 91	83 - 91
22	22	chain 'D' and (resid 92 through 106 )	D	D	92 - 106	92 - 106
23	23	chain 'D' and (resid 107 through 114 )	D	D	107 - 114	107 - 114
24	24	chain 'E' and (resid 226 through 247 )	E	E	226 - 247	1 - 22
25	25	chain 'E' and (resid 248 through 292 )	E	E	248 - 292	23 - 67
26	26	chain 'E' and (resid 293 through 337 )	E	E	293 - 337	68 - 108
27	27	chain 'E' and (resid 338 through 352 )	E	E	338 - 352	109 - 123
28	28	chain 'E' and (resid 353 through 407 )	E	E	353 - 407	124 - 169
29	29	chain 'E' and (resid 408 through 437 )	E	E	408 - 437	170 - 197
30	30	chain 'E' and (resid 438 through 484 )	E	E	438 - 484	198 - 244
31	31	chain 'E' and (resid 485 through 513 )	E	E	485 - 513	245 - 273
32	32	chain 'E' and (resid 514 through 531 )	E	E	514 - 531	274 - 291
33	33	chain 'F' and (resid 222 through 267 )	F	F	222 - 267	1 - 46
34	34	chain 'F' and (resid 268 through 292 )	F	F	268 - 292	47 - 71
35	35	chain 'F' and (resid 293 through 316 )	F	F	293 - 316	72 - 92
36	36	chain 'F' and (resid 317 through 363 )	F	F	317 - 363	93 - 139
37	37	chain 'F' and (resid 364 through 401 )	F	F	364 - 401	140 - 175
38	38	chain 'F' and (resid 402 through 421 )	F	F	402 - 421	176 - 195
39	39	chain 'F' and (resid 422 through 513 )	F	F	422 - 513	196 - 287
40	40	chain 'F' and (resid 514 through 530 )	F	F	514 - 530	288 - 304
41	41	chain 'G' and (resid 1 through 66 )	G	G	1 - 66	1 - 66
42	42	chain 'G' and (resid 67 through 90 )	G	G	67 - 90	67 - 90
43	43	chain 'G' and (resid 91 through 118 )	G	G	91 - 118	91 - 118
44	44	chain 'H' and (resid 1 through 7 )	H	H	1 - 7	1 - 7
45	45	chain 'H' and (resid 8 through 17 )	H	H	8 - 17	8 - 17
46	46	chain 'H' and (resid 18 through 32 )	H	H	18 - 32	18 - 32
47	47	chain 'H' and (resid 33 through 44 )	H	H	33 - 44	33 - 44
48	48	chain 'H' and (resid 45 through 59 )	H	H	45 - 59	45 - 59
49	49	chain 'H' and (resid 60 through 72 )	H	H	60 - 72	60 - 72
50	50	chain 'H' and (resid 73 through 82 )	H	H	73 - 82	73 - 82
51	51	chain 'H' and (resid 83 through 91 )	H	H	83 - 91	83 - 91
52	52	chain 'H' and (resid 92 through 98 )	H	H	92 - 98	92 - 98
53	53	chain 'H' and (resid 99 through 106 )	H	H	99 - 106	99 - 106
54	54	chain 'H' and (resid 107 through 115 )	H	H	107 - 115	107 - 115

+
About Yorodumi

-
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