[English] 日本語
Yorodumi
- PDB-2gtp: Crystal structure of the heterodimeric complex of human RGS1 and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gtp
TitleCrystal structure of the heterodimeric complex of human RGS1 and activated Gi alpha 1
Components
  • Guanine nucleotide-binding protein G(i), alpha-1 subunit
  • Regulator of G-protein signaling 1
KeywordsSIGNALING PROTEIN / G protein signalling / RGS / heterotrimeric G protein / signalling complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


leukotriene signaling pathway / positive regulation of GTPase activity / G-protein alpha-subunit binding / negative regulation of signal transduction / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E ...leukotriene signaling pathway / positive regulation of GTPase activity / G-protein alpha-subunit binding / negative regulation of signal transduction / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / GTPase activator activity / regulation of mitotic spindle organization / response to bacterium / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / cytoplasmic side of plasma membrane / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / heterotrimeric G-protein complex / G protein activity / midbody / cell cortex / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / calmodulin binding / Extra-nuclear estrogen signaling / immune response / ciliary basal body / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS domain / RGS domain profile. ...Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Regulator of G-protein signaling 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSoundararajan, M. / Turnbull, A.P. / Ugochukwu, E. / Gorrec, F. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural diversity in the RGS domain and its interaction with heterotrimeric G protein alpha-subunits.
Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / ...Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / Doyle, D.A. / Siderovski, D.P.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: 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_ref_seq_dif / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Guanine nucleotide-binding protein G(i), alpha-1 subunit
B: Guanine nucleotide-binding protein G(i), alpha-1 subunit
C: Regulator of G-protein signaling 1
D: Regulator of G-protein signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,35510
Polymers107,2144
Non-polymers1,1416
Water2,414134
1
A: Guanine nucleotide-binding protein G(i), alpha-1 subunit
D: Regulator of G-protein signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1775
Polymers53,6072
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanine nucleotide-binding protein G(i), alpha-1 subunit
C: Regulator of G-protein signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1775
Polymers53,6072
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.451, 102.904, 128.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUAA32 - 3481 - 317
21ARGARGLEULEUBB32 - 3481 - 317
12TRPTRPGLNGLNCC69 - 19122 - 144
22TRPTRPGLNGLNDD69 - 19122 - 144

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Guanine nucleotide-binding protein G(i), alpha-1 subunit / Adenylate cyclase-inhibiting G alpha protein


Mass: 37031.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: P63096
#2: Protein Regulator of G-protein signaling 1 / RGS1 / Early response protein 1R20 / B-cell activation protein BL34


Mass: 16575.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: Q08116

-
Non-polymers , 4 types, 140 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaNO3, 0.1M bis-Tris propane, pH 6.5, 20 % PEG3350, 10 % Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 39406 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.55→2.64 Å / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB IDs 2BV1 and 1Y3A used as starting models for RGS1 and GNAI1 respectively.

2bv1

1y3a


Resolution: 2.55→46.7 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.661 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.545 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27562 1976 5 %RANDOM
Rwork0.2259 ---
all0.22839 37274 --
obs0.22839 37274 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.466 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.44 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7007 0 68 134 7209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227207
X-RAY DIFFRACTIONr_bond_other_d0.0030.024720
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9569772
X-RAY DIFFRACTIONr_angle_other_deg0.964311517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6065886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46924.809341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.847151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0671533
X-RAY DIFFRACTIONr_chiral_restr0.0750.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028028
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021491
X-RAY DIFFRACTIONr_nbd_refined0.2150.21614
X-RAY DIFFRACTIONr_nbd_other0.1860.24817
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23645
X-RAY DIFFRACTIONr_nbtor_other0.0880.23714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2215
X-RAY DIFFRACTIONr_metal_ion_refined0.2110.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.23
X-RAY DIFFRACTIONr_mcbond_it0.3911.54571
X-RAY DIFFRACTIONr_mcbond_other0.1051.51794
X-RAY DIFFRACTIONr_mcangle_it0.66327128
X-RAY DIFFRACTIONr_scbond_it1.16433052
X-RAY DIFFRACTIONr_scangle_it1.724.52644
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1842tight positional0.070.05
2C732tight positional0.030.05
1A2204medium positional0.490.5
2C846medium positional0.270.5
1A1842tight thermal0.170.5
2C732tight thermal0.150.5
1A2204medium thermal0.452
2C846medium thermal0.292
LS refinement shellResolution: 2.55→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 136 -
Rwork0.292 2741 -
obs--98.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.86650.9861-1.21231.11920.10295.1109-0.127-0.04930.12760.16230.14170.674-0.0094-0.4248-0.01470.1011-0.01690.03680.0618-0.05820.023811.00238.24128.737
22.75590.6187-0.0513.46382.30642.65060.1023-0.2095-0.14160.0985-0.12660.3060.2266-0.3260.02420.1983-0.18230.02410.18660.02010.04053.92711.02322.62
30.86881.10750.33992.58160.28161.3515-0.04280.11460.1004-0.12260.03930.0906-0.0484-0.14120.00340.1588-0.03650.03420.1058-0.0126-0.004818.01935.3823.393
41.96840.147-0.00453.0003-0.52962.24750.0244-0.0941-0.05450.3850.0228-0.13540.07380.0867-0.04720.1567-0.03490.0050.1139-0.0366-0.033124.9330.1934.489
52.4553-1.89630.66981.47-0.61481.91110.1368-0.03710.5164-0.0546-0.1761-0.1891-0.23260.05250.03930.1744-0.04290.00370.0572-0.00710.0729-39.00218.65657.829
63.6533-1.99021.55624.1758-0.1715.95060.1237-0.19490.32240.0335-0.19970.0181-0.516-0.41060.0760.09750.1119-0.01020.194-0.09670.0327-59.2222.5550.848
72.0639-0.54750.30880.8699-0.34121.2470.02-0.18560.3723-0.0059-0.0705-0.2483-0.07120.06650.05050.1635-0.0401-0.01380.07-0.03570.0497-34.49415.66258.553
83.41210.3882-0.1331.5881-0.14962.37350.0543-0.2643-0.25420.0427-0.0566-0.02680.22630.07220.00230.1696-0.06330.00540.07430.0169-0.0036-39.940.00264.666
97.68872.13662.05413.329-3.16085.6397-0.19670.89051.5-0.74830.4996-0.2796-0.5470.3861-0.3030.4995-0.03280.23210.23630.22160.4057-25.55727.84438.102
106.39920.62536.90062.31940.00289.6747-0.10561.24790.1321-0.599-0.1137-0.0201-0.19231.01680.21930.3930.11590.07050.38050.0921-0.0242-33.79212.41929.977
114.494-5.4379-2.8018.52520.28556.69770.26550.749-0.11-0.3767-0.43590.32740.1877-0.14610.17040.12570.07970.00780.1817-0.0091-0.0726-38.7055.28837.757
125.1053.51262.50888.10262.3715.5453-0.06480.15510.5646-0.3253-0.2638-0.0246-0.5268-0.12820.32860.20110.10510.11180.07860.13620.0524-33.96919.3439.256
131.8552.06033.76065.22772.36348.7425-0.02420.31750.6113-0.91610.29451.638-0.211-1.9722-0.27030.34270.032-0.37280.70930.11940.5663-6.93937.0715.194
144.4547-0.94120.48276.60275.213910.28560.07180.5731-0.091-1.1534-0.05820.38750.2271-0.5111-0.01360.6902-0.1671-0.07390.17480.11550.032110.13730.775-3.103
152.91551.606-0.12028.2081-0.241210.8541-0.0070.225-0.1787-1.25020.3045-0.03961.5230.2083-0.29760.5838-0.1667-0.01810.1719-0.04750.02816.27423.0930.806
168.7745-0.9836-2.48543.51031.76527.5451-0.0947-0.20340.7046-0.39640.12581.0191-0.1781-1.042-0.03110.1984-0.1021-0.13990.33640.06950.3146-1.24734.47910.132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 591 - 28
2X-RAY DIFFRACTION2AA60 - 16829 - 137
3X-RAY DIFFRACTION3AA169 - 268138 - 237
4X-RAY DIFFRACTION4AA269 - 348238 - 317
5X-RAY DIFFRACTION5BB32 - 901 - 59
6X-RAY DIFFRACTION6BB91 - 15060 - 119
7X-RAY DIFFRACTION7BB151 - 221120 - 190
8X-RAY DIFFRACTION8BB222 - 348191 - 317
9X-RAY DIFFRACTION9CC60 - 9013 - 43
10X-RAY DIFFRACTION10CC91 - 12444 - 77
11X-RAY DIFFRACTION11CC125 - 14278 - 95
12X-RAY DIFFRACTION12CC143 - 19196 - 144
13X-RAY DIFFRACTION13DD60 - 9013 - 43
14X-RAY DIFFRACTION14DD91 - 13044 - 83
15X-RAY DIFFRACTION15DD131 - 15684 - 109
16X-RAY DIFFRACTION16DD157 - 191110 - 144

+
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