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- PDB-7alb: human GCH-GFRP stimulatory complex 7-deaza-GTP bound -

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Basic information

Entry
Database: PDB / ID: 7alb
Titlehuman GCH-GFRP stimulatory complex 7-deaza-GTP bound
Components(GTP cyclohydrolase ...) x 2
KeywordsHYDROLASE / GTP cyclohydrolase 1 / GTPCH1 / GTP cyclohydrolase I regulatory protein / GFRP / allosteric regulation / complex / allosteric regulator
Function / homology
Function and homology information


GTP cyclohydrolase binding / pteridine-containing compound biosynthetic process / dihydrobiopterin metabolic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity / neuromuscular process controlling posture / negative regulation of biosynthetic process / GTP-dependent protein binding / regulation of removal of superoxide radicals ...GTP cyclohydrolase binding / pteridine-containing compound biosynthetic process / dihydrobiopterin metabolic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity / neuromuscular process controlling posture / negative regulation of biosynthetic process / GTP-dependent protein binding / regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / neuron projection terminus / regulation of nitric oxide biosynthetic process / mitogen-activated protein kinase binding / dopamine biosynthetic process / negative regulation of cardiac muscle cell apoptotic process / response to pain / positive regulation of heart rate / response to type II interferon / negative regulation of cellular senescence / response to tumor necrosis factor / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / positive regulation of telomere maintenance via telomerase / nitric oxide biosynthetic process / negative regulation of blood pressure / positive regulation of nitric-oxide synthase activity / regulation of blood pressure / vasodilation / positive regulation of neuron apoptotic process / melanosome / cytoplasmic vesicle / protein-containing complex assembly / nuclear membrane / response to lipopolysaccharide / GTPase activity / calcium ion binding / dendrite / protein-containing complex binding / GTP binding / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
GTP cyclohydrolase I, feedback regulatory protein / GFRP superfamily / GTP cyclohydrolase I feedback regulatory protein (GFRP) / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Domain/homology
PHENYLALANINE / 7-deaza-GTP / GTP cyclohydrolase 1 feedback regulatory protein / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsEbenhoch, R. / Nar, H.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I.
Authors: Rebecca Ebenhoch / Simone Prinz / Susann Kaltwasser / Deryck J Mills / Robert Meinecke / Martin Rübbelke / Dirk Reinert / Margit Bauer / Lisa Weixler / Markus Zeeb / Janet Vonck / Herbert Nar /
Abstract: Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). ...Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). Besides other roles, BH4 functions as cofactor in neurotransmitter biosynthesis. The BH4 biosynthetic pathway and GCH1 have been identified as promising targets to treat pain disorders in patients. The function of mammalian GCH1s is regulated by a metabolic sensing mechanism involving a regulator protein, GCH1 feedback regulatory protein (GFRP). GFRP binds to GCH1 to form inhibited or activated complexes dependent on availability of cofactor ligands, BH4 and phenylalanine, respectively. We determined high-resolution structures of human GCH1-GFRP complexes by cryoelectron microscopy (cryo-EM). Cryo-EM revealed structural flexibility of specific and relevant surface lining loops, which previously was not detected by X-ray crystallography due to crystal packing effects. Further, we studied allosteric regulation of isolated GCH1 by X-ray crystallography. Using the combined structural information, we are able to obtain a comprehensive picture of the mechanism of allosteric regulation. Local rearrangements in the allosteric pocket upon BH4 binding result in drastic changes in the quaternary structure of the enzyme, leading to a more compact, tense form of the inhibited protein, and translocate to the active site, leading to an open, more flexible structure of its surroundings. Inhibition of the enzymatic activity is not a result of hindrance of substrate binding, but rather a consequence of accelerated substrate binding kinetics as shown by saturation transfer difference NMR (STD-NMR) and site-directed mutagenesis. We propose a dissociation rate controlled mechanism of allosteric, noncompetitive inhibition.
History
DepositionOct 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
F: GTP cyclohydrolase 1
G: GTP cyclohydrolase 1
H: GTP cyclohydrolase 1
I: GTP cyclohydrolase 1
J: GTP cyclohydrolase 1
K: GTP cyclohydrolase 1
L: GTP cyclohydrolase 1
M: GTP cyclohydrolase 1
N: GTP cyclohydrolase 1
O: GTP cyclohydrolase 1
P: GTP cyclohydrolase 1
Q: GTP cyclohydrolase 1
R: GTP cyclohydrolase 1
S: GTP cyclohydrolase 1
T: GTP cyclohydrolase 1
a: GTP cyclohydrolase 1 feedback regulatory protein
b: GTP cyclohydrolase 1 feedback regulatory protein
c: GTP cyclohydrolase 1 feedback regulatory protein
d: GTP cyclohydrolase 1 feedback regulatory protein
e: GTP cyclohydrolase 1 feedback regulatory protein
f: GTP cyclohydrolase 1 feedback regulatory protein
g: GTP cyclohydrolase 1 feedback regulatory protein
h: GTP cyclohydrolase 1 feedback regulatory protein
i: GTP cyclohydrolase 1 feedback regulatory protein
j: GTP cyclohydrolase 1 feedback regulatory protein
k: GTP cyclohydrolase 1 feedback regulatory protein
l: GTP cyclohydrolase 1 feedback regulatory protein
m: GTP cyclohydrolase 1 feedback regulatory protein
n: GTP cyclohydrolase 1 feedback regulatory protein
o: GTP cyclohydrolase 1 feedback regulatory protein
p: GTP cyclohydrolase 1 feedback regulatory protein
q: GTP cyclohydrolase 1 feedback regulatory protein
r: GTP cyclohydrolase 1 feedback regulatory protein
s: GTP cyclohydrolase 1 feedback regulatory protein
t: GTP cyclohydrolase 1 feedback regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)684,385100
Polymers669,32940
Non-polymers15,05660
Water16,754930
1
A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
F: GTP cyclohydrolase 1
G: GTP cyclohydrolase 1
H: GTP cyclohydrolase 1
I: GTP cyclohydrolase 1
J: GTP cyclohydrolase 1
a: GTP cyclohydrolase 1 feedback regulatory protein
b: GTP cyclohydrolase 1 feedback regulatory protein
c: GTP cyclohydrolase 1 feedback regulatory protein
d: GTP cyclohydrolase 1 feedback regulatory protein
e: GTP cyclohydrolase 1 feedback regulatory protein
f: GTP cyclohydrolase 1 feedback regulatory protein
g: GTP cyclohydrolase 1 feedback regulatory protein
h: GTP cyclohydrolase 1 feedback regulatory protein
i: GTP cyclohydrolase 1 feedback regulatory protein
j: GTP cyclohydrolase 1 feedback regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,19350
Polymers334,66520
Non-polymers7,52830
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79330 Å2
ΔGint-800 kcal/mol
Surface area87800 Å2
MethodPISA
2
K: GTP cyclohydrolase 1
L: GTP cyclohydrolase 1
M: GTP cyclohydrolase 1
N: GTP cyclohydrolase 1
O: GTP cyclohydrolase 1
P: GTP cyclohydrolase 1
Q: GTP cyclohydrolase 1
R: GTP cyclohydrolase 1
S: GTP cyclohydrolase 1
T: GTP cyclohydrolase 1
k: GTP cyclohydrolase 1 feedback regulatory protein
l: GTP cyclohydrolase 1 feedback regulatory protein
m: GTP cyclohydrolase 1 feedback regulatory protein
n: GTP cyclohydrolase 1 feedback regulatory protein
o: GTP cyclohydrolase 1 feedback regulatory protein
p: GTP cyclohydrolase 1 feedback regulatory protein
q: GTP cyclohydrolase 1 feedback regulatory protein
r: GTP cyclohydrolase 1 feedback regulatory protein
s: GTP cyclohydrolase 1 feedback regulatory protein
t: GTP cyclohydrolase 1 feedback regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,19350
Polymers334,66520
Non-polymers7,52830
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79300 Å2
ΔGint-792 kcal/mol
Surface area88150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.656, 116.137, 177.316
Angle α, β, γ (deg.)90.000, 94.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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GTP cyclohydrolase ... , 2 types, 40 molecules ABCDEFGHIJKLMNOPQRSTabcdefghij...

#1: Protein
GTP cyclohydrolase 1 / GTP cyclohydrolase I / GTP-CH-I


Mass: 23473.984 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCH1, DYT5, GCH / Production host: Escherichia coli (E. coli) / References: UniProt: P30793, GTP cyclohydrolase I
#2: Protein
GTP cyclohydrolase 1 feedback regulatory protein / GFRP / GTP cyclohydrolase I feedback regulatory protein / p35


Mass: 9992.483 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCHFR, GFRP / Production host: Escherichia coli (E. coli) / References: UniProt: P30047

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Non-polymers , 4 types, 990 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-QBQ / 7-deaza-GTP / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-4-oxidanylidene-3~{H}-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 522.192 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C11H17N4O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 930 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% MPD 0.2 ; NH4 Acet; 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.979→160.06 Å / Num. obs: 2125175 / % possible obs: 93.4 % / Redundancy: 5.2 % / CC1/2: 0.998 / Net I/σ(I): 7.9
Reflection shellResolution: 1.979→2.139 Å / Num. unique obs: 346319 / CC1/2: 0.26 / % possible all: 68.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (18-SEP-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IS8
Resolution: 1.979→160.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.183
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 3700 1.13 %RANDOM
Rwork0.2062 ---
obs0.2064 327093 72.5 %-
Displacement parametersBiso max: 97.51 Å2 / Biso mean: 33.85 Å2 / Biso min: 13.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.841 Å20 Å2-1.2188 Å2
2--1.5482 Å20 Å2
3----0.7072 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.979→160.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43488 0 900 930 45318
Biso mean--29.35 31.12 -
Num. residues----5478
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d16448SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes7900HARMONIC5
X-RAY DIFFRACTIONt_it45180HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5819SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact35087SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d45520HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg61763HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion16.43
LS refinement shellResolution: 1.98→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2247 97 1.48 %
Rwork0.2198 6445 -
all0.2198 6542 -
obs--10.31 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.16820.1893-0.07110.4952-0.50530.81070.0469-0.08580.21180.112-0.05470.0376-0.13270.10330.0079-0.0228-0.0383-0.0102-0.0253-0.06870.0234-72.084882.318166.0327
20.08120.23860.25480.5213-0.33341.23650.15370.0351-0.0819-0.15120.00130.00070.3907-0.0758-0.1550.07560.0054-0.0592-0.0488-0.0213-0.0692-10.6614-21.866622.5598
30.49140.0921-0.41240.0970.21131.2960.0279-0.05510.00110.1009-0.0034-0.07180.08380.2232-0.0245-0.04960.0054-0.04330.0303-0.0057-0.041-57.478658.525563.9276
40.3058-0.14270.47080.2695-0.11140.68620.03290.1145-0.0395-0.130.0299-0.13820.12980.2149-0.0628-0.01870.06220.02560.0449-0.0287-0.043714.4405-9.197119.347
50.052-0.02220.00140.0499-0.0114-0.00010.01160.04270.0298-0.0091-0.0148-0.00530.01010.01330.0032-0.02860.0212-0.02530.045-0.0051-0.0428-63.280643.980623.2713
60.16990.20920.22570.26030.22990.85320.00750.02150.0401-0.13790.0244-0.0847-0.14360.1584-0.032-0.0011-0.02110.01980.01660.0141-0.039810.697218.60719.5439
70.22620.0130.15410.08660.10050.2073-0.01160.05940.0907-0.07730.0097-0.0396-0.03570.15160.0019-0.0604-0.044-0.01420.04640.0346-0.0069-66.871273.787119.5004
80.0992-0.0203-0.01410.26010.51680.8574-0.01370.04460.0874-0.1218-0.01450.0823-0.1815-0.11890.02820.02480.0487-0.03750.0190.0225-0.0379-16.98523.761723.0102
90.1976-0.0120.08150.15610.2220.4235-0.04120.06840.1801-0.0673-0.01460.0864-0.1868-0.07740.0558-0.02180.0152-0.0423-0.03320.03180.0606-94.27782.481422.8827
100.43510.1218-0.48380.1268-0.11371.03590.01550.0968-0.0047-0.0907-0.00110.12280.0662-0.315-0.0144-0.0563-0.0249-0.05660.0829-0.0028-0.0445-30.3144-1.330124.5121
110.35650.0334-0.28960.03940.10941.2571-0.00750.04150.0643-0.0554-0.02010.17310.047-0.23570.0276-0.09950.0029-0.02530.039-0.01030.0475-110.830260.899724.4929
120.2780.2350.41640.24330.33520.6110.0762-0.103-0.05170.1446-0.03420.05730.1785-0.2023-0.0420.0164-0.0883-0.01680.04970.029-0.0677-19.7202-13.393569.6547
130.13710.05410.13910.336-0.10140.25840.05810.0412-0.0334-0.0561-0.02490.07140.2533-0.0354-0.03320.026-0.0181-0.02530.0086-0.0187-0.0168-94.461338.76722.0769
140.2174-0.0980.48520.2027-0.0930.59890.0161-0.06930.06130.0783-0.02550.0381-0.0534-0.20750.0095-0.0460.011-0.00140.1068-0.017-0.0394-22.069815.086769.8469
150.00480.01950.06420.2213-0.27951.08050.0118-0.05680.06940.05810.0059-0.0658-0.19530.0264-0.0177-0.0081-0.01-0.0277-0.0023-0.0164-0.03153.997326.08366.766
160.23140.0646-0.29240.07880.00951.00720.0175-0.03960.01710.07190.027-0.15170.010.2364-0.0445-0.07840.0098-0.04680.0579-0.0049-0.010122.49964.769564.9191
170.1625-0.24750.24540.23050.33511.2030.1635-0.0409-0.08040.14070.0075-0.09090.39770.0668-0.1710.07280.0031-0.0895-0.0520.0256-0.04168.1514-19.82866.8874
180.13010.09180.13430.4840.76831.4230.0811-0.0319-0.08750.2079-0.04050.01020.34340.0733-0.04060.0818-0.0064-0-0.04140.014-0.0771-75.703836.395165.8515
190.48820.23520.63050.22330.13710.86640.0841-0.15790.01580.1099-0.06060.15920.1693-0.2208-0.0235-0.0223-0.08740.07750.0354-0.0496-0.0384-101.653947.401169.3498
200.4386-0.13220.49360.1999-0.38211.1628-0.0095-0.14170.21440.1559-0.05660.1675-0.1196-0.23720.0661-0.06020.0090.04820.0015-0.1310.0452-99.644275.435969.4534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ N|* }N58 - 249
2X-RAY DIFFRACTION2{ A|* }A58 - 249
3X-RAY DIFFRACTION3{ O|* }O58 - 249
4X-RAY DIFFRACTION4{ B|* }B63 - 249
5X-RAY DIFFRACTION5{ P|* }P58 - 249
6X-RAY DIFFRACTION6{ C|* }C60 - 249
7X-RAY DIFFRACTION7{ Q|* }Q58 - 249
8X-RAY DIFFRACTION8{ D|* }D58 - 249
9X-RAY DIFFRACTION9{ R|* }R58 - 249
10X-RAY DIFFRACTION10{ E|* }E58 - 249
11X-RAY DIFFRACTION11{ S|* }S60 - 249
12X-RAY DIFFRACTION12{ F|* }F58 - 249
13X-RAY DIFFRACTION13{ T|* }T58 - 249
14X-RAY DIFFRACTION14{ G|* }G58 - 249
15X-RAY DIFFRACTION15{ H|* }H58 - 249
16X-RAY DIFFRACTION16{ I|* }I60 - 249
17X-RAY DIFFRACTION17{ J|* }J58 - 249
18X-RAY DIFFRACTION18{ K|* }K58 - 249
19X-RAY DIFFRACTION19{ L|* }L63 - 249
20X-RAY DIFFRACTION20{ M|* }M60 - 249

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