PDB-5o7x: CRYSTAL STRUCTURE OF S. CEREVISIAE CORE FACTOR AT 3.2A RESOLUTION

ID or keywords:

Entry

Database: PDB / ID: 5o7x

Title

CRYSTAL STRUCTURE OF S. CEREVISIAE CORE FACTOR AT 3.2A RESOLUTION

Components

RNA polymerase I-specific transcription initiation factor RRN11
RNA polymerase I-specific transcription initiation factor RRN6
RNA polymerase I-specific transcription initiation factor RRN7

Keywords

TRANSCRIPTION / RNA POLYMERASE I INITIATION / CORE FACTOR

Function / homology

Function and homology information

RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I /

transcription initiation at RNA polymerase I promoter / TBP-class protein binding /

nucleolus ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.2 Å

Authors

Engel, C. / Gubbey, T. / Neyer, S. / Sainsbury, S. / Oberthuer, C. / Baejen, C. / Bernecky, C. / Cramer, P.

Citation

Journal: Cell / Year: 2017
Title: Structural Basis of RNA Polymerase I Transcription Initiation.
Authors: Christoph Engel / Tobias Gubbey / Simon Neyer / Sarah Sainsbury / Christiane Oberthuer / Carlo Baejen / Carrie Bernecky / Patrick Cramer /

Abstract: Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron ...

History

Deposition	Jun 9, 2017	Deposition site: PDBE / Processing site: PDBE
Supersession	Aug 2, 2017	ID: 5N5X
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2017	Group: Structure summary / Category: pdbx_entry_details
Revision 1.2	Oct 16, 2019	Group: Data collection / Category: reflns_shell

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5o7x.cif.gz	3.2 MB	Display	PDBx/mmCIF format
PDB format	pdb5o7x.ent.gz	2.7 MB	Display	PDB format
PDBx/mmJSON format	5o7x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o7/5o7x ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o7x	HTTPS FTP

-
Related structure data

Related structure data	3590C 3591C 3592C 3593C 3594C 5n5yC 5n5zC 5n60C 5n61C C: citing same article (ref.)
Similar structure data	2xkx-d 2i4o-d 2181 3j2q-d 4j6m-d 3cp2-1 11029 6hbc-d 2i4m-d 4j6l-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: RNA polymerase I-specific transcription initiation factor RRN6

B: RNA polymerase I-specific transcription initiation factor RRN7

C: RNA polymerase I-specific transcription initiation factor RRN11

D: RNA polymerase I-specific transcription initiation factor RRN6

E: RNA polymerase I-specific transcription initiation factor RRN7

F: RNA polymerase I-specific transcription initiation factor RRN11

G: RNA polymerase I-specific transcription initiation factor RRN6

H: RNA polymerase I-specific transcription initiation factor RRN7

I: RNA polymerase I-specific transcription initiation factor RRN11

J: RNA polymerase I-specific transcription initiation factor RRN6

K: RNA polymerase I-specific transcription initiation factor RRN7

L: RNA polymerase I-specific transcription initiation factor RRN11

M: RNA polymerase I-specific transcription initiation factor RRN6

N: RNA polymerase I-specific transcription initiation factor RRN7

O: RNA polymerase I-specific transcription initiation factor RRN11

P: RNA polymerase I-specific transcription initiation factor RRN6

Q: RNA polymerase I-specific transcription initiation factor RRN7

R: RNA polymerase I-specific transcription initiation factor RRN11

hetero molecules

1.33 MDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA polymerase I-specific transcription initiation factor RRN6

B: RNA polymerase I-specific transcription initiation factor RRN7

C: RNA polymerase I-specific transcription initiation factor RRN11

hetero molecules

defined by software
Evidence: gel filtration
222 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: RNA polymerase I-specific transcription initiation factor RRN6

E: RNA polymerase I-specific transcription initiation factor RRN7

F: RNA polymerase I-specific transcription initiation factor RRN11

hetero molecules

defined by software
222 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: RNA polymerase I-specific transcription initiation factor RRN6

H: RNA polymerase I-specific transcription initiation factor RRN7

I: RNA polymerase I-specific transcription initiation factor RRN11

hetero molecules

defined by software
222 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: RNA polymerase I-specific transcription initiation factor RRN6

K: RNA polymerase I-specific transcription initiation factor RRN7

L: RNA polymerase I-specific transcription initiation factor RRN11

hetero molecules

defined by software
222 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

M: RNA polymerase I-specific transcription initiation factor RRN6

N: RNA polymerase I-specific transcription initiation factor RRN7

O: RNA polymerase I-specific transcription initiation factor RRN11

hetero molecules

defined by software
222 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

P: RNA polymerase I-specific transcription initiation factor RRN6

Q: RNA polymerase I-specific transcription initiation factor RRN7

R: RNA polymerase I-specific transcription initiation factor RRN11

hetero molecules

defined by software
222 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	109.070, 109.140, 385.640
Angle α, β, γ (deg.)	90.02, 90.01, 59.98
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	RNA polymerase I-specific transcription initiation factor RRN6 Mass: 102163.227 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32786
#2: Protein	RNA polymerase I-specific transcription initiation factor RRN7 Mass: 60435.195 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: RRN7, YJL025W, J1273 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40992
#3: Protein	RNA polymerase I-specific transcription initiation factor RRN11 Mass: 59334.262 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: RRN11, YML043C, YM9827.09C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04712
#4: Chemical	... ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 30 Source method: isolated from a genetically manipulated source Formula: SO₄ Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Formula: Mg Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli BL21(DE3) (bacteria)
Sequence details	Following the original deposition 5N5X, a frameshift was detected in blades I and II of the Rrn6 ...Following the original deposition 5N5X, a frameshift was detected in blades I and II of the Rrn6 beta-propeller domain using a new algorithm by T. Croll. The mistake in chains A, D, G, J, M and P (residues 169-281) has now been corrected and the structure was refined again as described in Engel et al., 2017.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.41 Å³/Da / Density % sol: 72.14 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 12% PEG 4000 , 500mM Ammonium sulfate, 100mM MES pH=6.0, 1mM DTT

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99998 Å / Relative weight: 1
Reflection	Resolution: 3.2→54.57 Å / Num. obs: 251223 / % possible obs: 98.9 % / Redundancy: 8.283 % / Net I/σ(I): 14.83

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.2→54.57 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 34.2

	R_factor	Num. reflection	% reflection
R_free	0.2828	7453	2.97 %
R_work	0.2544	-	-
obs	0.2553	251066	98.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.2→54.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	63438	0	0	0	63438

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	64782
X-RAY DIFFRACTION	f_angle_d	1.074	87510
X-RAY DIFFRACTION	f_dihedral_angle_d	21.214	39024
X-RAY DIFFRACTION	f_chiral_restr	0.054	9780
X-RAY DIFFRACTION	f_plane_restr	0.008	10914

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3105	X-RAY DIFFRACTION	POSITIONAL
1	2	D	3105	X-RAY DIFFRACTION	POSITIONAL	0.018
1	3	G	3105	X-RAY DIFFRACTION	POSITIONAL	0.019
1	4	J	3105	X-RAY DIFFRACTION	POSITIONAL	0.011
1	5	M	3105	X-RAY DIFFRACTION	POSITIONAL	0.019
1	6	P	3105	X-RAY DIFFRACTION	POSITIONAL	0.018
2	1	A	696	X-RAY DIFFRACTION	POSITIONAL
2	2	D	696	X-RAY DIFFRACTION	POSITIONAL	0.009
2	3	G	696	X-RAY DIFFRACTION	POSITIONAL	0.009
2	4	J	696	X-RAY DIFFRACTION	POSITIONAL	0.008
2	5	M	696	X-RAY DIFFRACTION	POSITIONAL	0.009
2	6	P	696	X-RAY DIFFRACTION	POSITIONAL	0.008
3	1	A	1055	X-RAY DIFFRACTION	POSITIONAL
3	2	D	1055	X-RAY DIFFRACTION	POSITIONAL	0.01
3	3	G	1055	X-RAY DIFFRACTION	POSITIONAL	0.01
3	4	J	1055	X-RAY DIFFRACTION	POSITIONAL	0.01
3	5	M	1055	X-RAY DIFFRACTION	POSITIONAL	0.01
3	6	P	1055	X-RAY DIFFRACTION	POSITIONAL	0.011
4	1	B	1919	X-RAY DIFFRACTION	POSITIONAL
4	2	E	1919	X-RAY DIFFRACTION	POSITIONAL	0.012
4	3	H	1919	X-RAY DIFFRACTION	POSITIONAL	0.012
4	4	K	1919	X-RAY DIFFRACTION	POSITIONAL	0.011
4	5	N	1919	X-RAY DIFFRACTION	POSITIONAL	0.012
4	6	Q	1919	X-RAY DIFFRACTION	POSITIONAL	0.012
5	1	B	1229	X-RAY DIFFRACTION	POSITIONAL
5	2	E	1229	X-RAY DIFFRACTION	POSITIONAL	0.01
5	3	H	1229	X-RAY DIFFRACTION	POSITIONAL	0.01
5	4	K	1229	X-RAY DIFFRACTION	POSITIONAL	0.01
5	5	N	1229	X-RAY DIFFRACTION	POSITIONAL	0.01
5	6	Q	1229	X-RAY DIFFRACTION	POSITIONAL	0.01
6	1	C	978	X-RAY DIFFRACTION	POSITIONAL
6	2	F	978	X-RAY DIFFRACTION	POSITIONAL	0.011
6	3	I	978	X-RAY DIFFRACTION	POSITIONAL	0.012
6	4	L	978	X-RAY DIFFRACTION	POSITIONAL	0.011
6	5	O	978	X-RAY DIFFRACTION	POSITIONAL	0.012
6	6	R	978	X-RAY DIFFRACTION	POSITIONAL	0.011
7	1	C	1557	X-RAY DIFFRACTION	POSITIONAL
7	2	F	1557	X-RAY DIFFRACTION	POSITIONAL	0.008
7	3	I	1557	X-RAY DIFFRACTION	POSITIONAL	0.009
7	4	L	1557	X-RAY DIFFRACTION	POSITIONAL	0.009
7	5	O	1557	X-RAY DIFFRACTION	POSITIONAL	0.009
7	6	R	1557	X-RAY DIFFRACTION	POSITIONAL	0.009

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 (%)
3.1999-3.2362	0.3823	228	0.3837	8046	X-RAY DIFFRACTION	99
3.2362-3.2743	0.3887	238	0.3781	8133	X-RAY DIFFRACTION	99
3.2743-3.3142	0.3926	258	0.3885	8330	X-RAY DIFFRACTION	99
3.3142-3.3562	0.4569	246	0.396	8035	X-RAY DIFFRACTION	99
3.3562-3.4003	0.3747	249	0.3777	8267	X-RAY DIFFRACTION	100
3.4003-3.4469	0.4064	199	0.3655	8125	X-RAY DIFFRACTION	99
3.4469-3.4961	0.3366	251	0.3444	8140	X-RAY DIFFRACTION	100
3.4961-3.5483	0.3491	253	0.345	8299	X-RAY DIFFRACTION	100
3.5483-3.6038	0.3761	242	0.3551	8131	X-RAY DIFFRACTION	100
3.6038-3.6628	0.3613	257	0.3351	8120	X-RAY DIFFRACTION	100
3.6628-3.726	0.3678	258	0.3285	8252	X-RAY DIFFRACTION	100
3.726-3.7937	0.372	253	0.3238	8199	X-RAY DIFFRACTION	100
3.7937-3.8667	0.3826	262	0.3237	8140	X-RAY DIFFRACTION	100
3.8667-3.9456	0.3526	251	0.3271	8148	X-RAY DIFFRACTION	99
3.9456-4.0313	0.3828	246	0.32	7657	X-RAY DIFFRACTION	92
4.0313-4.1251	0.3435	237	0.3069	7919	X-RAY DIFFRACTION	97
4.1251-4.2282	0.3054	251	0.2758	8189	X-RAY DIFFRACTION	100
4.2282-4.3425	0.3033	256	0.2646	8236	X-RAY DIFFRACTION	100
4.3425-4.4702	0.2815	247	0.2426	8118	X-RAY DIFFRACTION	100
4.4702-4.6144	0.2752	254	0.2399	8218	X-RAY DIFFRACTION	100
4.6144-4.7792	0.2692	259	0.2259	8252	X-RAY DIFFRACTION	100
4.7792-4.9705	0.2707	259	0.2176	8325	X-RAY DIFFRACTION	100
4.9705-5.1965	0.2371	250	0.2154	8148	X-RAY DIFFRACTION	100
5.1965-5.4703	0.2673	259	0.2446	8199	X-RAY DIFFRACTION	100
5.4703-5.8126	0.3027	255	0.2541	8071	X-RAY DIFFRACTION	99
5.8126-6.2608	0.3002	239	0.2434	7652	X-RAY DIFFRACTION	93
6.2608-6.8898	0.2874	260	0.2625	8202	X-RAY DIFFRACTION	100
6.8898-7.8842	0.2418	251	0.2137	8217	X-RAY DIFFRACTION	100
7.8842-9.9235	0.1983	257	0.1724	8242	X-RAY DIFFRACTION	100
9.9235-54.5779	0.2323	228	0.2274	7603	X-RAY DIFFRACTION	93

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	0.4364	-0.5348	0.259	2.1701	-0.952	2.4763	0.1783	0.1804	0.0283	-0.036	-0.3424	-0.0262	-0.2897	0.3943	-0.0361	1.1626	0.0443	-0.151	0.7724	-0.0571	1.0609	22.3717	68.8427	-124.7966
2	0.4491	-0.5432	-0.3025	2.1299	1.0179	2.4908	0.1776	0.1843	-0.0293	-0.0397	-0.3544	0.0109	0.2798	-0.3792	-0.0403	1.211	0.0393	0.1479	0.7522	0.0523	1.0599	-35.4106	6.1869	68.028
3	2.3444	-0.4039	-0.9889	0.4045	0.2069	2.4123	-0.2747	0.2546	-0.0331	0.0736	0.1199	-0.0297	0.4596	0.0859	-0.0375	0.8604	0.1625	0.0228	1.1045	0.1429	1.0456	6.1031	-3.1335	3.7542
4	1.2343	1.0621	-0.6868	1.413	-0.7578	2.3665	-0.1501	-0.1248	-0.0072	-0.3625	0.0048	-0.0318	0.1891	0.4063	-0.0382	0.9102	-0.2092	-0.1125	1.064	0.0874	1.0499	34.9859	28.1736	-60.5245
5	2.2744	-0.3905	0.9888	0.3866	-0.2396	2.5152	-0.2768	0.2941	0.0351	0.0865	0.112	0.0262	-0.4732	-0.0634	-0.0376	0.84	0.1503	-0.0287	1.1167	-0.1442	1.0561	-19.1239	78.2104	-189.0708
6	1.2398	1.0562	0.7096	1.439	0.766	2.4337	-0.1422	-0.1489	0.0124	-0.3527	-0.0226	0.0544	-0.1682	-0.451	-0.0431	0.8919	-0.2214	0.1181	1.0764	-0.0937	1.05	-47.9958	46.9379	-253.3429

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A or chain B or chain C
2	X-RAY DIFFRACTION	2	chain D or chain E or chain F
3	X-RAY DIFFRACTION	3	chain G or chain H or chain I
4	X-RAY DIFFRACTION	4	chain J or chain K or chain L
5	X-RAY DIFFRACTION	5	chain M or chain N or chain O
6	X-RAY DIFFRACTION	6	chain P or chain Q or chain R

-
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