PDB-9qr4: InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (inte...

ID or keywords:

Entry

Database: PDB / ID: 9qr4

Title

InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392

Components

Internalin B

Keywords

CELL INVASION / LEUCINE RICH REPEAT / PROTEIN BINDING / PATHOGENICITY / VIRULENCE FACTOR

Function / homology

Function and homology information

peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Listeria monocytogenes EGD-e (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Geerds, C. / Niemann, H.H.

Funding support

Germany, 1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Single mutations to tyrosine or glutamate improve crystallizability and crystal diffraction properties of a flexible two-domain protein
Authors: Geerds, C. / Niemann, H.H.

History

Deposition	Apr 3, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9qr4.cif.gz	803.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9qr4.ent.gz	559.3 KB	Display	PDB format
PDBx/mmJSON format	9qr4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9qr4_validation.pdf.gz	455.5 KB	Display	wwPDB validaton report
Full document	9qr4_full_validation.pdf.gz	460.7 KB	Display
Data in XML	9qr4_validation.xml.gz	62.7 KB	Display
Data in CIF	9qr4_validation.cif.gz	90.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qr/9qr4 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/9qr4	HTTPS FTP

-
Related structure data

Related structure data	9qr5C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/1174 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (4) #248 - Aug 2020 Phytosulfokine Receptor similarity (4) #245 - May 2020 Spliceosomes similarity (3) #60 - Dec 2004 Ubiquitin similarity (1) #105 - Sep 2008 Ribonuclease A similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (1) #68 - Aug 2005 Neurotrophins similarity (1)

Deposited unit

A: Internalin B

B: Internalin B

C: Internalin B

hetero molecules

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

1

A: Internalin B

hetero molecules

defined by author
Evidence: gel filtration
40.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Internalin B

hetero molecules

defined by author
Evidence: gel filtration
40.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Internalin B

hetero molecules

defined by author
Evidence: gel filtration
40.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.920, 149.170, 220.810
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Internalin B / InlB / Invasion protein InlB Mass: 40483.859 Da / Num. of mol.: 3 / Mutation: T336Y Source method: isolated from a genetically manipulated source Details: N-terminal residues GPLGS remain after proteolytic removal of the expression tag; point mutation T336Y Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Gene: inlB, lmo0434 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: P0DQD2
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1405 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.61 % Description: bipyramidal with a size of about 280 x 60 x 60 micrometer
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Reservoir solution: MORPHEUS Screen, Condition F3: 0.1 M mixture of imidazole and MES (acid) pH 6.5, 10% PEG4000, 20% glycerol, 0.02 M of each monosaccaharide: D-glucose, D-mannose, D- ...Details: Reservoir solution: MORPHEUS Screen, Condition F3: 0.1 M mixture of imidazole and MES (acid) pH 6.5, 10% PEG4000, 20% glycerol, 0.02 M of each monosaccaharide: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine. Protein buffer: 10 mM Tris pH 8.0, 20 mM NaCl. Protein concentration: 10 mg/ml. Drop size: 1 ul protein + 1 ul reservoir.

Crystal

Density Matthews: 3.05 Å³/Da / Density % sol: 59.61 %
Description: bipyramidal with a size of about 280 x 60 x 60 micrometer

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Reservoir solution: MORPHEUS Screen, Condition F3: 0.1 M mixture of imidazole and MES (acid) pH 6.5, 10% PEG4000, 20% glycerol, 0.02 M of each monosaccaharide: D-glucose, D-mannose, D- ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 18, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 192399 / % possible obs: 98 % / Redundancy: 13.33 % / B_iso Wilson estimate: 24.68 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.072 / Net I/σ(I): 19.04
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 12.46 % / Mean I/σ(I) obs: 2 / Num. unique obs: 13816 / CC_1/2: 0.627 / R_rim(I) all: 1.592 / % possible all: 96.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.21_5207	refinement
XDS	VERSION Jun 1, 2017 BUILT=20170923	data reduction
XSCALE	VERSION Jan 10, 2022 BUILT=20220220	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→20.13 Å / SU ML: 0.1606 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1959	9649	5.02 %
R_work	0.1728	182521	-
obs	0.174	192170	97.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 37.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→20.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8483	0	66	1405	9954

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	8935
X-RAY DIFFRACTION	f_angle_d	0.8653	12168
X-RAY DIFFRACTION	f_chiral_restr	0.0583	1415
X-RAY DIFFRACTION	f_plane_restr	0.0064	1552
X-RAY DIFFRACTION	f_dihedral_angle_d	12.0508	3398

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 (%)
1.6-1.62	0.3018	326	0.2854	5731	X-RAY DIFFRACTION	94.39
1.62-1.64	0.2944	316	0.2799	6011	X-RAY DIFFRACTION	97.76
1.64-1.66	0.2782	308	0.2737	5765	X-RAY DIFFRACTION	92.85
1.66-1.68	0.285	302	0.2597	5757	X-RAY DIFFRACTION	94.7
1.68-1.7	0.2714	283	0.2423	6001	X-RAY DIFFRACTION	97.88
1.7-1.72	0.2845	294	0.2306	6145	X-RAY DIFFRACTION	98.04
1.72-1.75	0.2526	296	0.2326	5968	X-RAY DIFFRACTION	98.09
1.75-1.78	0.256	327	0.2262	6043	X-RAY DIFFRACTION	98.15
1.78-1.8	0.2714	325	0.2191	6084	X-RAY DIFFRACTION	98.24
1.8-1.83	0.2333	296	0.212	6023	X-RAY DIFFRACTION	98.29
1.83-1.86	0.2274	330	0.2068	6116	X-RAY DIFFRACTION	98.47
1.86-1.9	0.2204	334	0.1983	6004	X-RAY DIFFRACTION	98.42
1.9-1.93	0.2089	327	0.1891	6092	X-RAY DIFFRACTION	98.59
1.93-1.97	0.2193	313	0.191	6078	X-RAY DIFFRACTION	98.57
1.97-2.02	0.2304	327	0.1876	6082	X-RAY DIFFRACTION	98.77
2.02-2.06	0.2379	322	0.1821	6103	X-RAY DIFFRACTION	98.68
2.06-2.12	0.2086	318	0.1751	6099	X-RAY DIFFRACTION	98.94
2.12-2.17	0.202	317	0.1726	6127	X-RAY DIFFRACTION	98.94
2.17-2.24	0.1876	319	0.1716	6172	X-RAY DIFFRACTION	99.04
2.24-2.31	0.1911	347	0.172	6057	X-RAY DIFFRACTION	98.71
2.31-2.39	0.2178	303	0.1666	5781	X-RAY DIFFRACTION	92.7
2.39-2.49	0.1978	356	0.162	6167	X-RAY DIFFRACTION	99.22
2.49-2.6	0.2063	305	0.1621	6188	X-RAY DIFFRACTION	99.33
2.6-2.74	0.1948	323	0.1624	6159	X-RAY DIFFRACTION	99.42
2.74-2.91	0.1821	361	0.1604	6214	X-RAY DIFFRACTION	99.47
2.91-3.13	0.1863	314	0.1651	6258	X-RAY DIFFRACTION	99.64
3.13-3.44	0.1755	336	0.1657	6314	X-RAY DIFFRACTION	99.73
3.44-3.94	0.1811	336	0.1569	6287	X-RAY DIFFRACTION	99.7
3.94-4.95	0.1514	304	0.1369	6110	X-RAY DIFFRACTION	94.9
4.95-20.13	0.1922	384	0.1844	6585	X-RAY DIFFRACTION	99.32

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	0.950033544065	0.553304470715	1.70618958814	0.962387801998	1.13489075572	3.76089201878	0.0128163981482	0.158636062073	-0.0199983951436	0.0731545037547	-0.0588767582397	-0.134919096018	-0.0234078118785	0.264925105411	0.0444808584145	0.476986919247	-0.0306277877359	-0.0885836145891	0.334217894142	0.0798214434647	0.376118117613	-15.4060527784	20.5725394428	-48.0787606614
2	1.21169531956	1.15047818121	-0.998764226753	2.99003667868	-1.62044461764	2.11669295663	0.136780412063	-0.153108082689	0.270728750256	0.295506024314	-0.0890615420731	0.593044250933	-0.501234029489	0.361614113095	-0.0918849570469	0.464984733683	-0.0921050050676	-0.059345439453	0.214196749958	0.036219731444	0.328546541573	-11.2244521119	25.672878054	-10.8602632856
3	0.266130033037	-0.0370714811185	0.242751247339	2.2676490503	-1.52894820321	1.13001445327	-0.0142764721713	-0.0166506822857	0.155854132321	-0.0246264913153	-0.0457229149042	0.183848962887	-0.286165227629	0.190134333238	0.00386907068301	0.34054135384	-0.0219222030466	-0.0334533120213	0.219062665878	0.0326173469339	0.271214044503	-10.3496761716	10.4829226106	-2.96267936782
4	2.77567481038	0.264998182161	0.147272316916	1.86854676481	0.60696199319	1.56143922495	0.0454293448838	-0.274303089766	-0.246643443283	0.0890540732152	0.028411575044	-0.0563297261747	0.231704850978	0.30298707039	-0.0292891075609	0.115169533941	0.0475407053987	0.0140492537406	0.196542822701	0.0108985958	0.150673348195	-10.7454418696	-13.306379228	9.42119434308
5	0.50746591738	0.184621403242	0.79584296936	1.17875769612	0.903482714491	1.80756988511	0.0160553991424	0.217365140346	-0.144898836834	-0.467300190314	-0.0389833960993	0.0807147482253	0.0094072941542	0.0988269712109	-0.325060617494	0.352884394783	0.0479966360289	-0.0440371525232	0.252535725969	-0.0634067046967	0.209395806377	-16.3871687317	-27.945735232	-45.719159253
6	1.63533071429	0.77703820501	-0.674803360805	2.22517513911	-1.06223862419	1.71051106324	0.0998948589859	-0.181264153897	-0.126716551393	0.0976542407503	-0.113716720686	-0.00216204397823	-0.0117883579393	0.194383041459	-0.0105101584782	0.151499091172	-0.000935784441959	-0.00811720871322	0.1455788928	0.0108582780476	0.180233702009	-12.5161318923	-23.5052397135	-5.71388755929
7	0.160401294805	-0.498505985941	0.237235151049	3.32367055177	-2.93663726837	2.94691516444	0.120785968837	0.0131736539657	-0.0221535799537	0.108856968376	-0.0863600387395	0.240536208942	-0.160851533996	0.190838554772	-0.0560177336765	0.118555824884	-0.030046738533	-0.00638354071095	0.14396945919	0.00596384146179	0.161641124326	-10.9210800726	-36.904933587	-2.47645440751
8	2.33191367928	0.845333741291	0.192794300536	0.314909434426	0.205232221503	2.6362361449	0.172638424836	-0.341490508864	-0.332538375651	0.00728008182823	-0.03739360752	-0.0875387455459	0.460539814632	0.756791075145	0.0275487712582	0.122566581943	0.0794372876127	-0.0116285817777	0.245457703577	0.0277579426074	0.174037032766	-10.9592007176	-60.0030380285	10.6034138184
9	1.35251649451	-0.425552635041	1.56290749632	0.416763629696	-1.04313151736	3.45910834734	0.0368846732021	-0.118162385184	-0.102050660081	0.0500549008742	0.072374429524	0.0413528080174	0.146352160717	-0.122200109627	-0.0560460908581	0.37459052294	0.0126426400617	-0.0443718453363	0.258666246508	0.0546663210624	0.278752524594	-24.7205418404	-6.11493733632	-55.958552876
10	0.576578025744	-0.0672487797776	0.74615042496	1.3587302442	-0.880320986967	3.34108602613	-0.00752938016177	-0.125959775662	-0.0478218811024	0.186754970579	0.0862393312398	-0.0116923480242	0.00273155453027	-0.18009836232	-0.0766977039192	0.198202815256	-0.0116992267578	-0.0310204898893	0.218600954588	0.0459498958775	0.21501733473	-35.3576459944	3.69419576144	-79.9717714285
11	1.41896020543	-0.470074892119	-0.250369973086	2.08409694416	0.391148568254	2.0515516471	0.0221104714832	0.163269673825	-0.100439957744	-0.181588123116	0.0111175325958	-0.15405176844	0.202837414196	-0.136851899208	-0.0491541808511	0.195473534065	-0.00804641165155	-0.0123055751123	0.167460943462	0.00806229363038	0.211433079099	-32.2147160973	4.01193147139	-105.815228173
12	1.49738859373	0.738452535787	0.38355672194	6.71992249539	3.94102043074	4.01762599958	-0.116902821152	0.0277427574982	-0.237945104881	-0.188857143848	0.462773422947	-0.413038996338	0.0873011070151	0.408835518966	-0.383169707929	0.269713720247	-1.87048638663E-5	-0.0191312960567	0.173543294052	0.0786910779012	0.233819092238	-32.0503229787	-3.63641797033	-103.196200818
13	7.47311031904	4.0088931369	2.9271251536	2.14879249854	1.57060228762	1.14651381277	0.765961437419	-1.25152573105	-1.23114080172	0.0935395488384	-0.253819121877	-0.887242008289	0.569534143895	-0.684160419298	-0.505566320609	0.673814191863	0.0544345010335	-0.135298729637	0.369424671485	0.0394202004608	0.5771343654	-37.9367411017	-24.9014472206	-114.525349696
14	2.80061597712	-0.081811246499	0.793364011959	2.28335592534	1.72311038232	1.56730940354	0.559089339121	0.423041002842	-2.68422187652	0.44978194137	0.553836771054	-1.54968823131	0.792906671049	0.437361967307	-0.000704217871345	0.917949578556	0.0273576841057	-0.182582176723	0.644568484167	-0.28590733126	1.45364392266	-34.6390830368	-32.685142734	-119.294480585
15	0.519669222113	-0.598891945614	-0.0213125833123	1.43115476185	0.649356633117	0.531017866447	0.122926750976	-0.699017399693	-0.0361009765184	-0.11327929636	0.302502221892	-0.504927356506	0.423491041468	0.474907512982	-0.362460134187	1.07756484544	0.300888767313	0.398186703512	0.710367567112	0.166881633795	1.60168624603	-41.5836391737	-41.0057504137	-121.301687459

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 35 through 223 )	A	A	35 - 223	1 - 189
2	2	chain 'A' and (resid 224 through 304 )	A	A	224 - 304	190 - 270
3	3	chain 'A' and (resid 305 through 339 )	A	A	305 - 339	271 - 305
4	4	chain 'A' and (resid 340 through 391 )	A	A	340 - 391	306 - 357
5	5	chain 'B' and (resid 35 through 244 )	B	E	35 - 244	1 - 210
6	6	chain 'B' and (resid 245 through 304 )	B	E	245 - 304	211 - 270
7	7	chain 'B' and (resid 305 through 339 )	B	E	305 - 339	271 - 305
8	8	chain 'B' and (resid 340 through 391 )	B	E	340 - 391	306 - 357
9	9	chain 'C' and (resid 32 through 157 )	C	K	32 - 157	1 - 126
10	10	chain 'C' and (resid 158 through 244 )	C	K	158 - 244	127 - 213
11	11	chain 'C' and (resid 245 through 304 )	C	K	245 - 304	214 - 273
12	12	chain 'C' and (resid 305 through 329 )	C	K	305 - 329	274 - 298
13	13	chain 'C' and (resid 330 through 349 )	C	K	330 - 349	299 - 318
14	14	chain 'C' and (resid 350 through 386 )	C	K	350 - 386	319 - 355
15	15	chain 'C' and (resid 387 through 389 )	C	K	387 - 389	356 - 358

-
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