PDB-3m0w: Structure of S100A4 with PCP

ID or keywords:

Entry

Database: PDB / ID: 3m0w

Title

Structure of S100A4 with PCP

Components

Protein S100-A4

Keywords

Calcium Binding Protein / MTS1 / S100 CALCIUM-BINDING PROTEIN A4 / S100A4 / METASTASIN

Function / homology

Function and homology information

RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / perinuclear region of cytoplasm ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Ramagopal, U.A. / Dulyaninova, N.G. / Almo, S.C. / Bresnick, A.R.

Citation

Journal: To be published
Title: Structure of S100A4 with PCP
Authors: Ramagopal, U.A. / Dulyaninova, N.G. / Almo, S.C. / Bresnick, A.R.

History

Deposition	Mar 3, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 12, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3m0w.cif.gz	199.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3m0w.ent.gz	158.8 KB	Display	PDB format
PDBx/mmJSON format	3m0w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3m0w_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	3m0w_full_validation.pdf.gz	3.5 MB	Display
Data in XML	3m0w_validation.xml.gz	35.7 KB	Display
Data in CIF	3m0w_validation.cif.gz	49 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m0/3m0w ftp://data.pdbj.org/pub/pdb/validation_reports/m0/3m0w	HTTPS FTP

-
Related structure data

Related structure data	2q91S S: Starting model for refinement
Similar structure data	6bzd-d 1oge-1 1ogf-1 1pdj-d 3igq-2 6tjm-1 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

2q91S

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein S100-A4

B: Protein S100-A4

C: Protein S100-A4

D: Protein S100-A4

E: Protein S100-A4

F: Protein S100-A4

G: Protein S100-A4

H: Protein S100-A4

I: Protein S100-A4

J: Protein S100-A4

hetero molecules

122 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: Protein S100-A4

B: Protein S100-A4

hetero molecules

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

3

C: Protein S100-A4

D: Protein S100-A4

hetero molecules

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

4

E: Protein S100-A4

F: Protein S100-A4

hetero molecules

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

5

G: Protein S100-A4

H: Protein S100-A4

hetero molecules

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

6

I: Protein S100-A4

J: Protein S100-A4

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.577, 102.275, 117.370
Angle α, β, γ (deg.)	90.000, 92.600, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 2 / Auth seq-ID: 3 - 90 / Label seq-ID: 2 - 89

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J

#1: Protein	Protein S100-A4 / S100 calcium-binding protein A4 / Metastasin / Protein Mts1 / Placental calcium-binding protein / Calvasculin Mass: 11614.342 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAPL, MTS1, S100A4 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3) / References: UniProt: P26447
#2: Chemical	ChemComp-P77 / 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine Mass: 373.943 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₀H₂₄ClN₃S / Comment: medication*YM
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₈O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.9793 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 2.8→25 Å / Num. obs: 31659 / % possible obs: 99.6 % / Redundancy: 3.2 % / R_merge(I) obs: 0.065 / Χ²: 1.046 / Net I/σ(I): 11.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.8-2.85	3.3	0.54	1582	1.15	1	100
2.85-2.9	3.3	0.46	1590	1.212	1	100
2.9-2.96	3.3	0.403	1553	1.164	1	100
2.96-3.02	3.3	0.353	1623	1.187	1	100
3.02-3.08	3.3	0.303	1555	1.121	1	100
3.08-3.15	3.3	0.258	1582	1.18	1	99.9
3.15-3.23	3.3	0.209	1580	1.162	1	100
3.23-3.32	3.3	0.176	1577	1.201	1	100
3.32-3.42	3.3	0.132	1604	1.087	1	100
3.42-3.53	3.2	0.108	1572	1.286	1	99.9
3.53-3.65	3.3	0.083	1601	1.026	1	100
3.65-3.8	3.2	0.07	1552	1.099	1	100
3.8-3.97	3.2	0.066	1591	1.071	1	99.7
3.97-4.18	3.2	0.054	1586	0.891	1	99.9
4.18-4.44	3.2	0.051	1590	0.864	1	99.8
4.44-4.78	3.2	0.045	1567	0.868	1	99.6
4.78-5.26	3.2	0.045	1596	0.81	1	99.8
5.26-6.01	3.1	0.044	1605	0.834	1	99.5
6.01-7.53	3.2	0.04	1592	0.839	1	99.7
7.53-25	3.2	0.036	1561	0.834	1	95.1

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
CBASS		data collection
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q91

2q91

Resolution: 2.8→24.98 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.897 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.028 / SU ML: 0.324 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.503 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.302	1589	5 %	RANDOM
R_work	0.252	-	-	-
obs	0.254	31599	99.31 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 165.35 Å² / B_iso mean: 48.683 Å² / B_iso min: 15.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.91 Å²	0 Å²	0.73 Å²
2-	-	0.66 Å²	0 Å²
3-	-	-	0.32 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→24.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7010	0	332	9	7351

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	7476
X-RAY DIFFRACTION	r_angle_refined_deg	1.212	2.022	10035
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.266	5	875
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.806	25.783	351
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.367	15	1297
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.667	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1077
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5557
X-RAY DIFFRACTION	r_mcbond_it	0.919	1.5	4430
X-RAY DIFFRACTION	r_mcangle_it	1.864	2	7056
X-RAY DIFFRACTION	r_scbond_it	3.381	3	3046
X-RAY DIFFRACTION	r_scangle_it	5.232	4.5	2979

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	332	TIGHT POSITIONAL	0.07	0.05
2	B	332	TIGHT POSITIONAL	0.09	0.05
3	C	332	TIGHT POSITIONAL	0.05	0.05
4	D	332	TIGHT POSITIONAL	0.05	0.05
5	E	332	TIGHT POSITIONAL	0.06	0.05
6	F	332	TIGHT POSITIONAL	0.06	0.05
7	G	332	TIGHT POSITIONAL	0.09	0.05
8	H	332	TIGHT POSITIONAL	0.08	0.05
9	I	332	TIGHT POSITIONAL	0.1	0.05
10	J	332	TIGHT POSITIONAL	0.11	0.05
1	A	269	MEDIUM POSITIONAL	0.17	0.5
2	B	269	MEDIUM POSITIONAL	0.14	0.5
3	C	269	MEDIUM POSITIONAL	0.09	0.5
4	D	269	MEDIUM POSITIONAL	0.1	0.5
5	E	269	MEDIUM POSITIONAL	0.11	0.5
6	F	269	MEDIUM POSITIONAL	0.11	0.5
7	G	269	MEDIUM POSITIONAL	0.12	0.5
8	H	269	MEDIUM POSITIONAL	0.18	0.5
9	I	269	MEDIUM POSITIONAL	0.22	0.5
10	J	269	MEDIUM POSITIONAL	0.36	0.5
1	A	332	TIGHT THERMAL	0.2	0.5
2	B	332	TIGHT THERMAL	0.33	0.5
3	C	332	TIGHT THERMAL	0.17	0.5
4	D	332	TIGHT THERMAL	0.15	0.5
5	E	332	TIGHT THERMAL	0.15	0.5
6	F	332	TIGHT THERMAL	0.19	0.5
7	G	332	TIGHT THERMAL	0.2	0.5
8	H	332	TIGHT THERMAL	0.25	0.5
9	I	332	TIGHT THERMAL	0.44	0.5
10	J	332	TIGHT THERMAL	0.49	0.5
1	A	269	MEDIUM THERMAL	0.26	2
2	B	269	MEDIUM THERMAL	0.35	2
3	C	269	MEDIUM THERMAL	0.22	2
4	D	269	MEDIUM THERMAL	0.22	2
5	E	269	MEDIUM THERMAL	0.22	2
6	F	269	MEDIUM THERMAL	0.23	2
7	G	269	MEDIUM THERMAL	0.24	2
8	H	269	MEDIUM THERMAL	0.29	2
9	I	269	MEDIUM THERMAL	0.63	2
10	J	269	MEDIUM THERMAL	0.6	2

LS refinement shell

Resolution: 2.8→2.872 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.389	132	-
R_work	0.315	2155	-
all	-	2287	-
obs	-	-	97.28 %

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	6.8281	-3.5459	-0.4333	7.1616	-0.6562	5.1806	0.5778	0.0279	0.6272	0.4159	-0.4934	-1.3339	-0.8602	1.4277	-0.0844	0.2053	-0.2478	-0.0182	0.4375	-0.1235	0.4366	30.289	10.358	51.156
2	4.478	-5.1249	-1.6398	6.9154	7.2073	6.9229	0.1182	-0.079	-0.6543	0.3979	-0.433	0.8358	-0.1493	-0.0996	0.3148	0.1461	-0.2029	0.1296	0.0484	-0.1889	0.3894	9.59	7.648	58.015
3	12.6775	-1.9423	8.4524	3.3246	-0.4172	7.1079	0.6547	-0.4731	2.2507	-0.5273	-0.5269	0.1382	-2.5887	-2.4954	-0.1278	1.6319	1.2734	0.8248	1.3295	0.5259	0.9857	2.977	27.894	33.502
4	10.5102	0.6131	3.6395	2.3647	0.3564	6.3166	1.0263	2.0629	1.9822	-0.3317	-0.3411	-0.6518	-1.9066	0.6978	-0.6852	1.2137	0.2885	0.6731	0.7651	0.5267	0.9883	23.331	27.367	24.182
5	8.9456	2.2412	4.7646	7.0082	4.1059	7.2972	1.2877	0.1765	0.2937	-1.1257	-1.9787	0.8091	-1.1469	-2.9582	0.691	0.5543	1.0373	-0.0264	2.3096	0.1664	0.2097	-4.835	9.91	6.888
6	4.3182	4.5733	-1.9898	5.3293	-2.5474	8.6555	0.6055	0.3353	-0.7967	-1.0695	-0.5382	-0.9312	-1.1211	-1.2942	-0.0673	0.5353	0.8487	0.2855	1.3381	0.7025	0.4735	15.338	6.713	0.177
7	13.8731	3.7797	-3.5273	4.6741	-3.6742	3.9596	-0.2847	1.4676	0.0361	-0.2551	0.5807	0.7167	0.6884	-1.7809	-0.296	0.2766	-0.3733	-0.0581	1.2465	-0.077	0.161	-2.653	-22.207	15.439
8	8.7828	2.169	-6.4597	2.3016	1.5483	12.3955	-0.4695	1.0104	-0.9143	-0.1814	0.3008	-0.5451	0.6263	-0.4914	0.1687	0.0786	-0.2302	0.0183	0.4173	-0.2016	0.1852	18.59	-23.411	12.685

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 90
2	X-RAY DIFFRACTION	2	B	2 - 90
3	X-RAY DIFFRACTION	3	C	2 - 90
4	X-RAY DIFFRACTION	4	D	2 - 90
5	X-RAY DIFFRACTION	5	E	2 - 90
6	X-RAY DIFFRACTION	6	F	2 - 90
7	X-RAY DIFFRACTION	7	G	2 - 90
8	X-RAY DIFFRACTION	8	H	2 - 90

-
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