[English] 日本語
Yorodumi
- PDB-2b0u: The Structure of the Follistatin:Activin Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b0u
TitleThe Structure of the Follistatin:Activin Complex
Components
  • Follistatin
  • Inhibin beta A chain
KeywordsSIGNALING PROTEIN / activin / follistatin / TGF-beta / morphogen / inhibin
Function / homology
Function and homology information


activin receptor antagonist activity / activin A complex / inhibin A complex / cardiac fibroblast cell development / enzyme activator complex / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin ...activin receptor antagonist activity / activin A complex / inhibin A complex / cardiac fibroblast cell development / enzyme activator complex / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / TGFBR3 regulates activin signaling / negative regulation of follicle-stimulating hormone secretion / type II activin receptor binding / progesterone secretion / striatal medium spiny neuron differentiation / Glycoprotein hormones / negative regulation of macrophage differentiation / ameloblast differentiation / cellular response to oxygen-glucose deprivation / positive regulation of follicle-stimulating hormone secretion / hemoglobin biosynthetic process / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / negative regulation of phosphorylation / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / pattern specification process / activin binding / Signaling by BMP / activin receptor signaling pathway / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / Signaling by Activin / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / mesodermal cell differentiation / heparan sulfate proteoglycan binding / cellular response to angiotensin / odontogenesis / positive regulation of transcription by RNA polymerase III / negative regulation of epithelial cell differentiation / hair follicle morphogenesis / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / roof of mouth development / female gonad development / eyelid development in camera-type eye / endodermal cell differentiation / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / peptide hormone binding / negative regulation of type II interferon production / keratinocyte proliferation / hair follicle development / positive regulation of collagen biosynthetic process / BMP signaling pathway / hematopoietic progenitor cell differentiation / ovarian follicle development / extrinsic apoptotic signaling pathway / positive regulation of protein metabolic process / positive regulation of erythrocyte differentiation / erythrocyte differentiation / skeletal system development / cytokine activity / growth factor activity / negative regulation of cell growth / hormone activity / response to organic cyclic compound / defense response / cytokine-mediated signaling pathway / autophagy / male gonad development / cell-cell signaling / nervous system development / cellular response to hypoxia / transcription by RNA polymerase II / positive regulation of ERK1 and ERK2 cascade / cell differentiation / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Follistatin, N-terminal / : / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Inhibin, beta A subunit / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. ...Follistatin, N-terminal / : / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Inhibin, beta A subunit / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Kazal type serine protease inhibitors / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Cystine-knot cytokine / Ribbon / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IRIDIUM (III) ION / MALONATE ION / Inhibin beta A chain / Follistatin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / MIRAS / Resolution: 2.8 Å
AuthorsThompson, T.B. / Lerch, T.F. / Cook, R.W. / Woodruff, T.K. / Jardetzky, T.S.
CitationJournal: Dev.Cell / Year: 2005
Title: The Structure of the Follistatin:Activin Complex Reveals Antagonism of Both Type I and Type II Receptor Binding.
Authors: Thompson, T.B. / Lerch, T.F. / Cook, R.W. / Woodruff, T.K. / Jardetzky, T.S.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Version format compliance
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inhibin beta A chain
B: Inhibin beta A chain
C: Follistatin
D: Follistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,65614
Polymers89,1684
Non-polymers1,48710
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-97 kcal/mol
Surface area40100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.250, 120.820, 70.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Inhibin beta A chain / Activin beta-A chain / Erythroid differentiation protein / EDF


Mass: 12991.865 Da / Num. of mol.: 2 / Fragment: Activin (mature form)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Cell (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08476
#2: Protein Follistatin / FS / Activin-binding protein


Mass: 31592.205 Da / Num. of mol.: 2 / Fragment: Follistatin-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FST / Cell (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19883

-
Non-polymers , 4 types, 151 molecules

#3: Chemical
ChemComp-IR3 / IRIDIUM (III) ION


Mass: 192.217 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ir
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, 200 mM Malonate, pH 7.0, vapor diffusion, hanging drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97923 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.8→19.35 Å / Num. all: 23605 / Num. obs: 23416 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Phasing

PhasingMethod: MIRAS
Phasing set
IDCell angle alpha (°)Cell angle beta (°)Cell angle gamma (°)Cell length a (Å)Cell length b (Å)Cell length c (Å)D res high (Å)D res low (Å)
MIRAS909090109.25120.8270.572.819.35
1
Phasing MIRResolution: 2.8→29.66 Å / FOM acentric: 0.224 / FOM centric: 0.199 / Reflection acentric: 20139 / Reflection centric: 2620
Phasing MIR der

Der set-ID: 1 / Resolution: 2.8→29.66 Å

IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_10000200422564
ISO_20.9830.9670.2680.244106051613
ISO_30.9470.9370.4560.39599481535
ISO_40.9770.9780.4520.457117001737
ISO_50.9910.9790.1120.093128341853
ISO_60.9920.9930.2020.1635467977
ISO_70.970.9480.3450.37473291182
ISO_80.9880.9790.1010.089130491849
ISO_91.1381.0470.2540.2467251129
ANO_11000200140
ANO_20.96900.3860107020
ANO_30.90100.7330100400
ANO_40.8800.7840117970
ANO_50.99500.1440129150
ANO_60.98400.252055630
ANO_70.9800.297071410
ANO_80.99500.1710131410
ANO_90.95200.502068210
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
7.6929.66ISO_10000717243
5.537.69ISO_100001530283
4.545.53ISO_100002013295
3.944.54ISO_100002448326
3.533.94ISO_100002841351
3.233.53ISO_100003198359
2.993.23ISO_100003549360
2.82.99ISO_100003746347
7.6929.66ANO_110006910
5.537.69ANO_1100015300
4.545.53ANO_1100020130
3.944.54ANO_1100024480
3.533.94ANO_1100028410
3.233.53ANO_1100031980
2.993.23ANO_1100035470
2.82.99ANO_1100037460
7.6929.66ISO_20.9270.8970.5140.414717231
5.537.69ISO_20.9770.9860.3670.2651530283
4.545.53ISO_210.9830.2090.1482013295
3.944.54ISO_20.9980.9710.1390.1072448326
3.533.94ISO_20.9750.9570.1270.0992841351
3.233.53ISO_20.9640.9420.1140.0931056127
2.993.23ISO_2000000
2.82.99ISO_2000000
7.6929.66ANO_20.67901.57208140
5.537.69ANO_20.80901.081015300
4.545.53ANO_20.93600.547020130
3.944.54ANO_20.99100.258024480
3.533.94ANO_20.99900.111028410
3.233.53ANO_2100.074010560
2.993.23ANO_2000000
2.82.99ANO_2000000
7.6929.66ISO_30.8380.8540.8850.669717231
5.537.69ISO_30.910.9230.6510.4721530283
4.545.53ISO_30.960.960.3620.2462013295
3.944.54ISO_30.9810.9610.220.1732448326
3.533.94ISO_30.9830.9630.180.1372841351
3.233.53ISO_30.9771.010.1660.13539949
2.993.23ISO_3000000
2.82.99ISO_3000000
7.6929.66ANO_30.42703.10508130
5.537.69ANO_30.57802.156015300
4.545.53ANO_30.83100.978020130
3.944.54ANO_30.97900.423024480
3.533.94ANO_30.99700.175028410
3.233.53ANO_3100.1203950
2.993.23ANO_3000000
2.82.99ANO_3000000
7.6929.66ISO_40.9610.9911.0080.824717231
5.537.69ISO_40.9650.9450.6630.5181530283
4.545.53ISO_40.9890.9710.2680.1992013295
3.944.54ISO_40.9890.9670.1470.1032448326
3.533.94ISO_40.960.9450.1110.0862841351
3.233.53ISO_40.9430.9380.0940.0742151251
2.993.23ISO_4000000
2.82.99ISO_4000000
7.6929.66ANO_40.62801.7908140
5.537.69ANO_40.63401.779015300
4.545.53ANO_40.8500.842020130
3.944.54ANO_40.97500.36024480
3.533.94ANO_40.99800.145028410
3.233.53ANO_4100.078021510
2.993.23ANO_4000000
2.82.99ANO_4000000
7.6929.66ISO_50.9330.9310.1850.14717231
5.537.69ISO_50.980.9750.1560.1071530283
4.545.53ISO_51.0030.9880.10.072013295
3.944.54ISO_51.0040.9810.0770.0582448326
3.533.94ISO_50.9940.970.0750.0552841351
3.233.53ISO_50.9760.9580.0820.0673181355
2.993.23ISO_50.941.0510.0850.08610412
2.82.99ISO_5000000
7.6929.66ANO_50.91500.64608130
5.537.69ANO_50.94200.476015300
4.545.53ANO_50.9800.293020130
3.944.54ANO_50.99700.16024480
3.533.94ANO_50.99900.08028410
3.233.53ANO_5100.046031660
2.993.23ANO_5100.05301040
2.82.99ANO_5000000
7.6929.66ISO_60.9850.9760.3150.23717231
5.537.69ISO_60.9810.9590.2340.1551530283
4.545.53ISO_60.9850.9770.10.0682013295
3.944.54ISO_60.9870.9870.060.0441207168
3.533.94ISO_6000000
3.233.53ISO_6000000
2.993.23ISO_6000000
2.82.99ISO_6000000
7.6929.66ANO_60.89500.66308130
5.537.69ANO_60.9600.392015300
4.545.53ANO_60.99900.119020130
3.944.54ANO_6100.047012070
3.533.94ANO_6000000
3.233.53ANO_6000000
2.993.23ANO_6000000
2.82.99ANO_6000000
7.6929.66ISO_70.8530.840.8270.623717231
5.537.69ISO_70.9350.9270.5890.4291530283
4.545.53ISO_70.9850.9810.2460.172013295
3.944.54ISO_70.9931.0270.0920.0792316294
3.533.94ISO_70.9990.9780.0240.02975379
3.233.53ISO_7000000
2.993.23ISO_7000000
2.82.99ISO_7000000
7.6929.66ANO_70.55702.15808140
5.537.69ANO_70.85500.918015300
4.545.53ANO_70.99100.214020130
3.944.54ANO_70.99900.053022400
3.533.94ANO_7100.02205440
3.233.53ANO_7000000
2.993.23ANO_7000000
2.82.99ANO_7000000
7.6929.66ISO_80.9350.940.1670.135717231
5.537.69ISO_80.9820.9720.150.1131530283
4.545.53ISO_80.9960.9810.0910.0622013294
3.944.54ISO_810.9790.0620.0472448323
3.533.94ISO_80.9870.9660.0560.0432841344
3.233.53ISO_80.9820.9630.0520.0413198351
2.993.23ISO_80.9711.0020.0550.03230223
2.82.99ISO_8000000
7.6929.66ANO_80.93600.56908130
5.537.69ANO_80.94200.553015300
4.545.53ANO_80.98700.322020130
3.944.54ANO_80.99900.161024480
3.533.94ANO_8100.075028410
3.233.53ANO_8100.042031950
2.993.23ANO_8100.03603010
2.82.99ANO_8000000
7.6929.66ISO_91.021.0480.3710.297717231
5.537.69ISO_91.0830.980.3130.2681530283
4.545.53ISO_91.1591.0290.230.2132013295
3.944.54ISO_91.2031.0530.170.1632292293
3.533.94ISO_91.2581.3280.1470.1517327
3.233.53ISO_9000000
2.993.23ISO_9000000
2.82.99ISO_9000000
7.6929.66ANO_90.80101.11708140
5.537.69ANO_90.900.771015300
4.545.53ANO_90.95100.476020130
3.944.54ANO_90.98900.277022910
3.533.94ANO_90.99800.16501730
3.233.53ANO_9000000
2.993.23ANO_9000000
2.82.99ANO_9000000
Phasing MIR der site

Der-ID: ISO_1

IDBiso (Å)Cartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolOccupancy
199.2467.76212.73114.485Pt0.39
2269.5588.60335.55233.689Pt0.33
3261.859.90354.2710.964Pt0.47
4263.0832.03646.26617.694Pt0.01
53003.18519.85631.62Pt0.28
6187.3222.49321.02924.419Pt0.16
7299.9572.07529.46811.411Pt0.34
874.2754.79317.85728.891Pt0.07
9111.8567.14916.4911.729Os0.7
10204.868.10951.5630.727Os0.72
11252.4288.0949.43719.168Os0.69
12134.9969.35339.51215.865Os0.37
13114.0437.0634.59542.045Os0.15
14227.0283.61699.425.856Os0.28
15120.6228.81432.45620.865Os0.26
16130.3815.2786.22242.088Os0.23
17205.748.96747.5968.942Ir0.82
18236.5432.48745.44117.3Ir0.58
1965.9266.93815.91211.796Ir0.1
20160.731.662012.554Ir0.39
21248.9954.76013.38Ir0.3
22158.6847.0830.7859.689Ir0.27
23101.4869.57814.14844.868Ir0.14
24224.8518.4872.74361.89Ir0.23
2530016.65812.28767.43Ir0.48
26205.2267.11414.5231.941Ir0.29
27300105.6129.06926.069Ir0.35
2851.756.3522.61929.425Pb0.11
2986.1978.1439.26123.116Pb0.08
30181.5189.32625.2996.693Pb0.14
31260.3586.6848.49819.862Pb0.14
32183.8237.118114.74118.349Pb0.09
33209.3768.27751.3930.398Pb0.13
3460.7948.69548.0088.476Pb0.02
3530099.23115.20431.135Ir0.11
36300103.76813.20661.857Ir0.17
37206.6767.78250.62230.758Ir0.21
383088.08714.12452.977Ir0.01
393033.32746.28617.593Ir0.01
40215.9387.7269.55719.583Ir0.2
41210.1468.21251.19230.827Os0.81
42186.1788.1169.15719.555Os0.72
43239.9667.34316.52212.145Os0.51
443050.14947.7128.2Os0.01
45191.0714.45721.13155.115Os0.22
46276.4825.44121.55426.047Os0.38
47113.8766.98316.33611.618Au0.18
48169.3369.74523.7411.848Au0.1
493076.889-34.54670.624Au0.01
5067.3576.5440.82227.24Au0.05
5186.8948.9666.18615.638Au0.05
5252.0973.5991.74815.528Au0.64
53103.4269.8814.71418.652Au0.95
Phasing MIR shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
7.69-29.660.950.697814299
5.53-7.690.8390.461530283
4.54-5.530.5810.2622013295
3.94-4.540.3030.1742448326
3.53-3.940.1380.1032841351
3.23-3.530.0440.0373198359
2.99-3.230.0010.0013549360
2.8-2.99003746347

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHARPphasing
CNSrefinement
PDB_EXTRACT1.401data extraction
MAR345data collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→19.35 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1177 5 %thin shells
Rwork0.265 ---
all0.301 23381 --
obs0.301 23416 98.9 %-
Displacement parametersBiso mean: 30.103 Å2
Baniso -1Baniso -2Baniso -3
1-3.017 Å20 Å20 Å2
2--1.856 Å20 Å2
3----4.873 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5863 0 41 141 6045

+
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more