PDB-7sqp: Single chain trimer HLA-A*02:01 (Y108C) with HPV.16 E7 peptide YM...

ID or keywords:

Entry

Database: PDB / ID: 7sqp

Title

Single chain trimer HLA-A*02:01 (Y108C) with HPV.16 E7 peptide YMLDLQPETTDL

Components

Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
VHH

Keywords

IMMUNE SYSTEM / HLA / VHH / HPV / SCT

Function / homology

Function and homology information

symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated suppression of host cGAS-STING signal transduction / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host cell cycle progression / symbiont-mediated suppression of host apoptosis / positive regulation of actin filament polymerization / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / cadmium ion binding / antigen processing and presentation of peptide antigen via MHC class I / viral process ...
Similarity search - Function

Biological species

Human papillomavirus type 16

Pongo pygmaeus (Bornean orangutan)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.53 Å

Authors

Finton, K.A.K. / Rupert, P.B.

Funding support

United States, 1items

Citation

Journal: Front Immunol / Year: 2023
Title: Effects of HLA single chain trimer design on peptide presentation and stability.
Authors: Finton, K.A.K. / Rupert, P.B. / Friend, D.J. / Dinca, A. / Lovelace, E.S. / Buerger, M. / Rusnac, D.V. / Foote-McNabb, U. / Chour, W. / Heath, J.R. / Campbell, J.S. / Pierce, R.H. / Strong, R.K.

History

Deposition	Nov 5, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 31, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7sqp.cif.gz	474.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7sqp.ent.gz	319.8 KB	Display	PDB format
PDBx/mmJSON format	7sqp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7sqp_validation.pdf.gz	458.9 KB	Display	wwPDB validaton report
Full document	7sqp_full_validation.pdf.gz	464.7 KB	Display
Data in XML	7sqp_validation.xml.gz	34.8 KB	Display
Data in CIF	7sqp_validation.cif.gz	48 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sq/7sqp ftp://data.pdbj.org/pub/pdb/validation_reports/sq/7sqp	HTTPS FTP

-
Related structure data

Related structure data	7sr0C 7sr3C 7sr4C 7sr5C 7srkC 7sshC 7st3C 7stgC 1jf1S 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (2) #63 - Mar 2005 T-Cell Receptor similarity (2)

Deposited unit

A: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

B: VHH

C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

D: VHH

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

1

A: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

B: VHH

defined by author
Evidence: surface plasmon resonance
60.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

D: VHH

defined by author
60.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	117.979, 117.979, 262.706
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw

#1: Protein	Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera Mass: 47948.629 Da / Num. of mol.: 2 / Mutation: Y108C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 16, (gene. exp.) Pongo pygmaeus (Bornean orangutan), (gene. exp.) Homo sapiens (human) Gene: E7, B2M, HLA-A / Cell line (production host): HEK293F / Production host: Homo sapiens (human) References: UniProt: P03129, UniProt: P16213, UniProt: A0A678ZGP6
#2: Antibody	VHH Mass: 12536.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.03 Å³/Da / Density % sol: 69.44 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 200 mM NH4Citrate, 20.0% PEG 3350

-
Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.53→50 Å / Num. obs: 61220 / % possible obs: 97.93 % / Redundancy: 9.3 % / B_iso Wilson estimate: 56.23 Å² / CC_1/2: 0.997 / Net I/σ(I): 33.9
Reflection shell	Resolution: 2.53→2.62 Å / Num. unique obs: 5234 / CC_1/2: 0.997

-
Processing

Software

Name: CrysalisPro / Version: 1.19.1_4122 / Classification: data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1JF1

1jf1

Resolution: 2.53→48.96 Å / SU ML: 0.3514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2601	3089	5.05 %
R_work	0.2387	58084	-
obs	0.2398	61173	97.95 %

Solvent computation

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

Displacement parameters

B_iso mean: 67.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.53→48.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7503	0	0	108	7611

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0016	7698
X-RAY DIFFRACTION	f_angle_d	0.4868	10497
X-RAY DIFFRACTION	f_chiral_restr	0.0395	1133
X-RAY DIFFRACTION	f_plane_restr	0.005	1363
X-RAY DIFFRACTION	f_dihedral_angle_d	4.3037	1089

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 (%)
2.53-2.57	0.3856	96	0.3476	2030	X-RAY DIFFRACTION	76.15
2.57-2.62	0.3581	125	0.3026	2451	X-RAY DIFFRACTION	92.76
2.62-2.66	0.2876	131	0.2931	2504	X-RAY DIFFRACTION	94.95
2.66-2.71	0.3546	158	0.2894	2532	X-RAY DIFFRACTION	96.42
2.71-2.76	0.3497	153	0.2867	2577	X-RAY DIFFRACTION	97.36
2.76-2.82	0.3153	145	0.2886	2633	X-RAY DIFFRACTION	99.14
2.82-2.88	0.284	165	0.299	2629	X-RAY DIFFRACTION	99.43
2.88-2.95	0.377	125	0.3058	2659	X-RAY DIFFRACTION	99.82
2.95-3.02	0.3653	139	0.3241	2661	X-RAY DIFFRACTION	99.82
3.02-3.1	0.3834	132	0.2928	2697	X-RAY DIFFRACTION	99.89
3.1-3.19	0.3068	142	0.2651	2638	X-RAY DIFFRACTION	99.93
3.19-3.3	0.2543	146	0.2611	2677	X-RAY DIFFRACTION	99.96
3.3-3.41	0.2727	136	0.254	2672	X-RAY DIFFRACTION	99.93
3.41-3.55	0.2746	149	0.2552	2697	X-RAY DIFFRACTION	99.96
3.55-3.71	0.2337	129	0.2512	2694	X-RAY DIFFRACTION	100
3.71-3.91	0.2416	141	0.2161	2688	X-RAY DIFFRACTION	99.96
3.91-4.15	0.2274	138	0.2055	2712	X-RAY DIFFRACTION	100
4.15-4.47	0.2094	151	0.1948	2715	X-RAY DIFFRACTION	99.97
4.47-4.92	0.2093	150	0.1856	2726	X-RAY DIFFRACTION	99.93
4.92-5.63	0.197	132	0.2049	2775	X-RAY DIFFRACTION	99.97
5.63-7.09	0.2507	131	0.2372	2804	X-RAY DIFFRACTION	100
7.09-48.96	0.2689	175	0.2358	2913	X-RAY DIFFRACTION	98.91

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	2.93950675322	-0.910826834539	-0.849038261747	0.844529269381	0.533728880413	0.252383550259	-0.434299046926	-0.473565778578	-0.392856754826	0.199946796578	0.219727875462	0.064822052171	0.0421285535353	0.273657788916	0.16291167631	0.545585399024	0.138998907357	0.0897760795087	0.533195161054	0.132854194468	0.382728721494	-13.630754641	-31.5321084171	-24.1887711126
2	2.93778710689	-0.737830211211	-0.652068543416	1.38644261709	0.325419120852	1.47320937723	-0.138464636436	0.235512389613	-0.308257340516	0.087760459186	0.00347776940194	0.222069327044	-0.187571471155	-0.107149986526	0.100252500355	0.478719579111	0.0243851235607	0.0695294851452	0.436054887605	-0.0110796033354	0.469382369463	-4.38476404069	-37.9897511582	-39.1193994853
3	0.949655946246	0.0533118926847	0.0385752102614	1.22725631412	0.0417379555166	1.51857781275	-0.370251303103	0.47250671113	-0.87839011923	-0.177852215931	-0.0799774024414	0.362693701931	0.934417571022	-0.00856627898751	0.265604210639	0.942507738898	0.316499663009	0.343354732738	0.835777140322	0.150749769942	0.883535565605	-11.8316270182	-49.5521507352	-10.7886647237
4	7.04862877899	-1.16918699942	0.611030866186	3.54168762191	2.37292986234	1.91417174669	-0.0875092404862	-0.350467373455	0.0376012051237	-0.0733237761373	0.395740025116	0.180350398542	0.488327183676	0.060636253788	-0.141936999134	0.597396651229	0.0664551086792	0.0209774457781	0.602053627837	-0.0148276866632	0.393439060882	-40.0716659738	-15.8848539745	-14.496370553
5	1.82003643681	0.859356959854	-0.310666317597	1.94622324654	0.00602673370955	1.84654266624	-0.436598497666	-0.283623833021	1.28837849209	0.131894181322	0.700607356993	0.331637905232	-0.84245751375	0.0966802682003	0.192592601803	0.336759761541	0.0974914572023	-0.0276083150654	0.51954023165	0.157392834785	0.569703836089	-38.7579982784	-5.95401387737	-27.4034255282
6	0.707289068242	-0.35519494069	0.873307771856	0.181473115346	-0.440886005122	1.07522637784	-0.475527530218	-0.574771786354	0.0553478291821	0.634283288189	0.0427540165713	-0.202237414431	0.417550777828	0.115436679465	-0.0797469058327	0.875814947307	0.207224045844	-0.0703679504688	1.57117386506	0.00720092840756	0.893430370565	-33.3179353919	-14.828038743	-3.96217807112
7	2.71392083577	-0.311599708962	-0.391099137833	2.45188309552	-0.948005463226	1.06757643809	-0.287931084105	-0.0957004430468	0.0193753712946	-0.436384852564	0.0998613703663	0.0516606028149	0.246044841338	0.255044163934	0.0289605070446	0.486441858602	0.0632682280013	-0.0135638659554	0.480641240397	0.0289340760608	0.452495905141	-30.5011930699	-18.3408817435	-24.3428952982
8	2.01684512602	0.191097246936	1.40046948001	2.12099064971	-0.719870067111	3.1392258253	0.187272213425	-0.0196094717843	0.671111786356	0.00516103460314	0.249328101664	-0.312245696828	-0.0985452470212	0.536525622852	0.0377336928391	0.493436586674	0.0438234119817	-0.0939370318251	0.564144177387	-0.0281510670663	0.583815792874	-25.2548755656	-8.83825915215	-22.7554191167
9	2.6667791742	-0.00391164016835	-1.69974207793	3.33738286697	-0.182859782809	1.12740080882	0.478566135177	-0.882844302251	0.985036877524	0.618387419693	0.391683334918	0.236815863765	-0.195523626525	0.419272588387	-0.074909289658	0.534270697277	0.057398342759	0.102243805611	0.643916101484	-0.14487017762	0.696981243709	-32.9986339775	-6.48896430701	-16.3628447099
10	2.5523785709	-0.209664403779	0.570191733784	1.31316082702	-0.617242142887	1.2420089735	-0.163753999749	-0.366922559721	0.11397202081	0.0352542189151	0.327623849571	0.269031189141	-0.0535954936978	-0.0359255195977	4.43153584375E-5	0.557417105873	0.139690778637	-0.00871598461656	0.470117924196	0.00332622491725	0.423658975805	-33.1462652969	-16.8427144577	-22.7169988022
11	5.28326038326	0.400639158016	-0.00389031978805	4.99814587679	0.747034496376	0.137465032815	-0.574669991255	0.861498793167	0.661874918441	-0.993967257092	0.134523300399	-0.00893969928041	0.277848111899	-9.9611267238E-5	-0.0622003681862	0.439002732041	-0.011380560417	-0.0931722048268	0.654033509917	0.125828954255	0.504753858935	-40.8797558659	-11.0554467588	-34.0504607107
12	2.93432953048	0.979634685009	1.11419141039	1.28461437276	0.540752281289	1.06193984038	-0.348202508203	0.211499425497	0.477018321753	-0.146333675536	0.124149509541	0.149589553188	-0.02304838931	0.131059366281	0.177798781335	0.445968423398	-0.0780304458886	-0.0765407898149	0.389240436665	0.0586464641483	0.407946588374	-11.6988382233	30.772530801	-42.2052251535
13	4.13950824035	1.37775521506	0.780856491938	1.40227670213	0.453142094513	1.69799473789	-0.253882450339	-0.582128349728	0.686060814975	-0.0222309780869	-0.0275653619663	0.308605731353	0.0819162830452	-0.148087963276	0.188832310595	0.448472263402	0.040688306183	-0.0946012269459	0.459688591315	-0.09491059256	0.550319244939	-2.10806204504	38.2911490505	-27.3592755167
14	0.493946347631	-0.608845114567	-0.46893175952	1.21421317403	0.0360722243395	0.58234551717	-0.956403597841	0.539156576522	1.57546493167	-0.533460223356	0.582860845547	0.423641061431	-0.620563493095	0.173707962367	0.0268908969076	0.985510608947	-0.453834938114	-0.615765505428	0.684364064836	0.537682458103	1.36607412171	-10.2377808941	48.8160567758	-54.7110469459
15	6.34478038767	0.791114165272	-0.360129712994	4.02206501364	2.02305772364	1.10989238814	-0.0276167305764	-0.00852244373349	-0.274335462796	0.103338674398	0.139323302657	0.623768475689	-0.335045950815	-0.162579566743	-0.157174703757	0.501159235715	-0.0509357440874	0.009725242923	0.579132153562	-0.0490041262891	0.603759407288	-37.8996195396	14.0625539631	-50.27274997
16	4.97303576206	-1.97965258581	1.60034771834	2.72790780123	-0.129247303954	0.66504612166	-0.426469677562	-0.268815183355	-0.0270504885871	0.497954024602	-0.0869152293419	0.216374154147	0.294387002118	-0.14674142258	0.0880689952743	0.616953978181	0.0391951450541	0.114101047817	0.536734709651	0.0674368492783	0.598634201314	-37.5994253843	5.11898332003	-29.5514604855
17	1.21331215128	-0.335916822343	-0.0231904094473	2.12450644113	-1.59685321024	5.09859471872	-0.416828941927	0.690899204254	-0.201253073815	-0.720841158246	0.864777827408	0.443382016693	0.420216325223	0.811907331476	0.0894885261755	0.473450423152	-0.160382104285	0.0160504761595	0.584439774881	0.0083596937348	0.568838525679	-34.9692450825	6.65487136543	-43.7161857422
18	0.451082870629	-0.737848529768	0.135018961633	3.1700074188	-1.06773753509	0.404549697928	-0.577980245587	0.95983958007	0.24607909656	-0.609840808769	-0.0505736833224	-0.246017116042	-0.176417423529	0.214604392224	0.0313174957762	0.897833319652	-0.55148917296	0.0118864733418	1.67805221924	-0.181547687328	0.782677530861	-32.104397371	12.8041294713	-60.1394839612
19	1.86621046618	0.373595641588	-0.612790823653	1.57340169676	-0.146521375527	2.22938996373	-0.241633140686	0.160122946118	0.112718631718	-0.372030359385	0.00761258934838	0.117139299035	-0.0856971058823	-0.354086868493	0.119998838641	0.47669970346	-0.144333085561	0.0600895276027	0.456025793093	0.00402457319252	0.548983548193	-28.7822476757	15.3896593192	-44.5259481547
20	2.46576025974	-0.604394627065	0.868362665667	5.99485633896	0.523638566092	1.53399428876	-0.376014917649	-0.531679473797	-0.0289131178282	1.10454476914	0.0743560740943	0.110023994769	-0.0402478288101	-0.359445359073	0.185095351514	0.641035724426	-0.0271787479526	0.0371976524774	0.506481736014	0.00959275856721	0.477060310975	-27.9886197224	19.9688464914	-37.776893756
21	0.988805337403	-0.248161179366	-1.34863561357	1.49050131052	-0.621688230639	4.50476160868	0.0410110531435	-0.248627228854	-0.394808330135	-0.0718333297115	0.0980824806137	-0.546774274357	0.488468259822	0.0958126122686	0.0848825557844	0.41771031526	-0.0438686981064	0.126282342851	0.463018813221	0.014110187712	0.566374947551	-22.8806119619	8.36309335466	-41.3989807565
22	3.34000950377	0.365199901759	2.10685375437	4.27823987214	-0.771902273731	3.72859382511	0.108943860845	0.315702726452	-0.0355783945513	-0.580983791808	0.63287154242	-0.182371412344	-0.131674502566	0.39259351636	-0.0754054282448	0.408217549725	-0.0620898661202	0.00959581506428	0.516425595192	0.00229930442335	0.487755754563	-30.6199146543	5.24125003138	-47.0312191503
23	1.88429873537	-2.68217363985	-0.744336408466	4.90252098435	0.937231788539	0.403888076038	-0.0796331027268	-0.131500156991	-0.201190821869	0.94769878825	-0.00975959797745	-0.247835508585	-0.138112457325	0.843468289038	-0.0922533790994	0.726532583898	0.0718737952146	0.147546353282	0.60305354552	0.0508699407543	0.688143227936	-30.8028969301	9.51763638934	-27.966388857
24	2.02739251579	0.137118566773	-2.0109109061	0.781514674138	-0.288006579844	3.57807490121	0.0797441939216	0.425562262618	-0.201067414914	-0.214449634108	0.152380240093	0.609956634392	0.0734425187622	-0.553179082389	0.172809359108	0.526980538414	-0.066207348215	0.0890763826919	0.38523510534	0.0472033897038	0.426464817202	-32.2098304586	16.8072845183	-42.5512611454
25	2.79922799182	0.388824283102	-1.47691541596	1.4221287446	-0.36911338977	2.49972775442	-0.240310728071	0.238750635644	0.395407210489	-0.0487797004316	0.271477525714	0.402917990192	-0.319377334065	-0.0996333288197	0.136968981741	0.480716722418	-0.144057368109	0.0093003608383	0.494029355785	-0.0141896744973	0.536507634291	-32.874959565	17.6847524921	-45.3624212804

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 1 through 155 )	A	A	1 - 155	1 - 124
2	2	chain 'A' and (resid 156 through 340 )	A	A	156 - 340	125 - 309
3	3	chain 'A' and (resid 341 through 417 )	A	A	341 - 417	310 - 382
4	4	chain 'B' and (resid 3 through 9 )	B	B	3 - 9	1 - 7
5	5	chain 'B' and (resid 10 through 26 )	B	B	10 - 26	8 - 24
6	6	chain 'B' and (resid 27 through 32 )	B	B	27 - 32	25 - 30
7	7	chain 'B' and (resid 33 through 53 )	B	B	33 - 53	31 - 51
8	8	chain 'B' and (resid 54 through 74 )	B	B	54 - 74	52 - 72
9	9	chain 'B' and (resid 75 through 84 )	B	B	75 - 84	73 - 82
10	10	chain 'B' and (resid 85 through 111 )	B	B	85 - 111	83 - 109
11	11	chain 'B' and (resid 112 through 118 )	B	B	112 - 118	110 - 116
12	12	chain 'C' and (resid 1 through 155 )	C	C	1 - 155	1 - 123
13	13	chain 'C' and (resid 156 through 341 )	C	C	156 - 341	124 - 307
14	14	chain 'C' and (resid 342 through 417 )	C	C	342 - 417	308 - 380
15	15	chain 'D' and (resid 3 through 9 )	D	D	3 - 9	1 - 7
16	16	chain 'D' and (resid 10 through 19 )	D	D	10 - 19	8 - 17
17	17	chain 'D' and (resid 20 through 26 )	D	D	20 - 26	18 - 24
18	18	chain 'D' and (resid 27 through 32 )	D	D	27 - 32	25 - 30
19	19	chain 'D' and (resid 33 through 41 )	D	D	33 - 41	31 - 39
20	20	chain 'D' and (resid 42 through 53 )	D	D	42 - 53	40 - 51
21	21	chain 'D' and (resid 54 through 74 )	D	D	54 - 74	52 - 72
22	22	chain 'D' and (resid 75 through 84 )	D	D	75 - 84	73 - 82
23	23	chain 'D' and (resid 85 through 92 )	D	D	85 - 92	83 - 90
24	24	chain 'D' and (resid 93 through 100 )	D	D	93 - 100	91 - 98
25	25	chain 'D' and (resid 101 through 117 )	D	D	101 - 117	99 - 115

-
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