[English] 日本語
Yorodumi
- PDB-6y32: Structure of the GTPase heterodimer of human SRP54 and SRalpha -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y32
TitleStructure of the GTPase heterodimer of human SRP54 and SRalpha
Components(Signal recognition particle ...) x 2
KeywordsRNA BINDING PROTEIN / SRP54 NG domain / SR alpha NG domain / Targeting complex Protein translocation
Function / homology
Function and homology information


signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / cotranslational protein targeting to membrane / protein targeting to ER / signal-recognition-particle GTPase / XBP1(S) activates chaperone genes ...signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / cotranslational protein targeting to membrane / protein targeting to ER / signal-recognition-particle GTPase / XBP1(S) activates chaperone genes / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / neutrophil chemotaxis / intracellular protein transport / GDP binding / nuclear speck / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP54 subunit, eukaryotic / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle ...Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP54 subunit, eukaryotic / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Longin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Signal recognition particle receptor subunit alpha / Signal recognition particle subunit SRP54
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJuaire, K.D. / Becker, M.M.M. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586/6-1 Germany
CitationJournal: Structure / Year: 2021
Title: Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia.
Authors: Juaire, K.D. / Lapouge, K. / Becker, M.M.M. / Kotova, I. / Michelhans, M. / Carapito, R. / Wild, K. / Bahram, S. / Sinning, I.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal recognition particle 54 kDa protein
B: Signal recognition particle receptor subunit alpha
C: Signal recognition particle 54 kDa protein
D: Signal recognition particle receptor subunit alpha
E: Signal recognition particle 54 kDa protein
F: Signal recognition particle receptor subunit alpha
G: Signal recognition particle 54 kDa protein
H: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,70338
Polymers271,9868
Non-polymers5,71730
Water8,395466
1
A: Signal recognition particle 54 kDa protein
B: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3789
Polymers67,9972
Non-polymers1,3817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-54 kcal/mol
Surface area24320 Å2
MethodPISA
2
C: Signal recognition particle 54 kDa protein
D: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2828
Polymers67,9972
Non-polymers1,2856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-62 kcal/mol
Surface area23920 Å2
MethodPISA
3
E: Signal recognition particle 54 kDa protein
F: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3789
Polymers67,9972
Non-polymers1,3817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-61 kcal/mol
Surface area24300 Å2
MethodPISA
4
G: Signal recognition particle 54 kDa protein
H: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,66612
Polymers67,9972
Non-polymers1,66910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-89 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.825, 70.634, 172.573
Angle α, β, γ (deg.)90.000, 116.810, 90.000
Int Tables number3
Space group name H-MP121

-
Components

-
Signal recognition particle ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Signal recognition particle 54 kDa protein / SRP54


Mass: 33511.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP54 / Production host: Escherichia coli (E. coli) / References: UniProt: P61011
#2: Protein
Signal recognition particle receptor subunit alpha / SR-alpha / Docking protein alpha / DP-alpha


Mass: 34484.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPRA, SRPR / Production host: Escherichia coli (E. coli) / References: UniProt: P08240

-
Non-polymers , 4 types, 496 molecules

#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.4 M lithium sulfate, 13% (w/v) PEG 3350, 0.1 M Tris (pH 8.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.26
ReflectionResolution: 2.4→49.553 Å / Num. obs: 130686 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rpim(I) all: 0.06233 / Net I/σ(I): 11.34
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 12547 / Rpim(I) all: 0.6239

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3Q

5l3q


Resolution: 2.6→49.553 Å / Cross valid method: THROUGHOUT / σ(F): 97.23 / Phase error: 28.98
RfactorNum. reflection% reflection
Rfree0.1844 5184 5.02 %
Rwork0.149 --
obs0.1543 103314 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.99 Å2 / Biso mean: 59.3332 Å2 / Biso min: 13.07 Å2
Refinement stepCycle: final / Resolution: 2.6→49.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17559 0 334 466 18359
Biso mean--52.81 47.48 -
Num. residues----2288
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.64480.2672520.24184849510195
2.6448-2.69290.27062820.23634872515494
2.6929-2.74470.28542580.23194877513595
2.7447-2.80070.27812530.21414862511595
2.8007-2.86160.25492650.21574865513094
2.8616-2.92820.2682610.21014913517495
2.9282-3.00140.24232560.20124857511395
3.0014-3.08250.23852220.19374900512295
3.0825-3.17320.23432680.1924870513894
3.1732-3.27560.22932600.18314864512495
3.2756-3.39260.22172660.17324930519695
3.3926-3.52840.19342420.15854911515395
3.5284-3.68890.17922650.15274869513494
3.6889-3.88330.17812590.13974902516195
3.8833-4.12640.1662460.12534921516794
4.1264-4.44470.14792560.11714905516194
4.4447-4.89150.12672640.11114943520795
4.8915-5.59820.14962490.12194955520495
5.5982-7.04860.17832700.14094973524394
7.0486-44.49780.1462670.12115112537994
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)
10.58360.50440.51560.51570.68071.1539-0.08840.18390.0029-0.18340.01070.2122-0.0318-0.13060.04791.0417-0.0762-0.11320.26870.0450.3855130.338113.296441.3066
20.64760.0779-0.06081.2430.00060.5981-0.0070.03660.2404-0.17490.03330.4494-0.1126-0.2035-0.01991.1190.0508-0.04460.00250.00940.4445130.644740.926653.1762
30.5853-0.58040.18254.0754-0.75850.1528-0.076-0.1463-0.31080.35140.0606-0.44160.18520.10420.04851.01730.0297-0.05460.09970.02970.4648152.0615.05658.4299
41.14120.35080.46190.57670.10640.8393-0.0442-0.0748-0.04980.07360.0476-0.0484-0.10190.1009-0.04681.01240.00760.0804-0.0284-0.07290.2169159.125645.581762.4525
50.25840.2362-0.11510.9251-0.00610.71640.04120.0603-0.0509-0.0129-0.0081-0.08160.06070.0606-0.01271.04510.01540.0764-0.1276-0.05760.1773156.68534.041255.6306
60.1139-0.6370.61693.5762-3.44133.3276-0.0706-0.4432-0.5538-0.126-0.1203-0.15020.23730.23020.17691.04880.05890.05620.69630.18650.9323170.26355.0717106.1115
72.05940.24650.71610.99160.40851.9111-0.077-0.0958-0.46150.19830.0764-0.38430.31080.3425-0.02580.84910.0738-0.02940.4320.06670.4696181.227417.9395101.7337
80.7103-0.18680.03671.348-0.27480.7359-0.02490.02330.2660.117-0.0504-0.2824-0.17160.2390.04991.0448-0.099-0.0220.12770.04230.3801176.629244.499389.1005
91.4069-0.91280.11252.4829-0.46880.3598-0.0665-0.1825-0.09820.3007-0.023-0.127-0.03720.11930.08760.8903-0.0478-0.08470.15220.06360.2338176.227931.27101.368
101.94940.4282-0.64230.1536-0.05430.3339-0.30920.1782-0.5452-0.45320.2053-0.6160.3067-0.11980.11520.9701-0.024-0.01790.1669-0.03850.663159.03683.796793.6152
111.3457-1.2503-1.54551.16181.43561.77520.08220.0968-0.13140.7556-0.24581.12380.6562-0.57150.15760.9529-0.1266-0.01530.29720.11880.8328151.9316.047996.5163
122.7064-2.63841.7222.5722-1.67941.09640.2820.3229-0.5716-0.7176-0.2641.07810.2478-0.2868-0.00511.0846-0.1702-0.01290.5125-0.08710.9784150.64386.482286.6813
130.629-1.10310.35183.8171-0.41051.0632-0.0198-0.0497-0.77630.11770.12110.80730.4332-0.4425-0.09470.8045-0.04850.02230.80270.04850.8428135.412933.913288.7957
140.28580.0474-0.00820.908-0.15220.47480.0438-0.02720.07920.11060.0440.117-0.0859-0.1446-0.07491.10920.0010.1592-0.10040.12160.2151149.215544.473994.812
151.2196-0.21790.00312.4648-0.70641.61940.0151-0.0373-0.20490.05610.01170.21750.2892-0.1014-0.02250.8873-0.04830.05610.0552-0.02550.1394151.818327.62390.0091
161.2414-0.8198-0.45977.22222.6731.9431-0.0985-0.34880.70030.576-0.1623-0.0837-0.9573-0.0890.26571.0376-0.0145-0.02630.3886-0.1210.6703179.686151.071933.9543
171.77270.37560.15552.0741-0.35281.6241-0.331-0.10040.1970.18810.17530.4172-0.2843-0.37070.12270.80930.12740.12620.49530.0490.2992168.535438.989429.3547
181.37660.4978-0.10411.4814-0.21870.42020.02380.0063-0.38350.299-0.05970.13770.2017-0.18270.0740.8606-0.11610.15640.0971-0.05850.2811175.41737.871620.7089
193.14670.3779-2.1551.9724-1.77844.6538-0.08180.4876-0.44770.10160.06150.79870.7254-0.84740.02780.6904-0.16250.08380.557-0.1930.5966168.1573.143310.8425
201.114-0.5206-0.35910.5990.24381.4738-0.07820.2538-0.1139-0.0652-0.02380.2430.2268-0.32430.05240.786-0.04660.10610.20920.01270.1535173.541719.735913.1359
211.283-0.7492-0.49082.8706-0.37160.4464-0.0285-0.0690.00860.3750.12410.2291-0.1353-0.1037-0.05950.8761-0.0090.17780.16730.00490.2312174.273525.539328.9318
222.97162.23522.04471.89841.65161.4679-0.3278-0.06710.5903-0.03620.1090.2494-0.2906-0.07250.20011.17380.00190.06890.23740.02880.6779191.64155.457321.6625
232.95612.5422-0.45894.45470.13930.19610.04770.28790.6055-0.40650.106-0.5289-0.59080.161-0.18291.0694-0.08410.16680.22130.00990.6159198.511749.321119.0419
241.35-0.9135-0.04191.10950.7941.9046-0.0743-0.01320.2929-0.08760.2702-0.4326-0.12030.4177-0.22790.8225-0.02690.09520.0452-0.08460.2541206.173716.00717.9559
250.0579-0.1797-0.52560.70511.48884.7002-0.02860.0606-0.2312-0.05170.2522-0.25230.48280.5653-0.22640.79160.05130.00350.2068-0.1590.3697201.66343.174111.4182
260.32960.10680.04561.03840.47390.9684-0.0214-0.05640.010.14960.0868-0.18390.00460.1155-0.1091.09260.01090.0513-0.0368-0.0980.2128199.83321.933923.6783
271.76062.17391.5842.98422.7053.2998-0.2907-0.54010.83150.5221-0.3552-0.0062-1.0367-0.32370.63070.96980.0332-0.03660.5251-0.12420.6165100.347151.198231.725
284.2066-0.9633-1.04534.78921.10144.974-0.0449-0.15150.4654-0.04080.05020.2124-0.6019-0.30370.02760.74030.03360.07850.36650.00340.420793.558545.967724.2578
291.89180.60120.32874.31321.29841.8526-0.1021-0.36470.12340.0803-0.07580.4662-0.1915-0.4470.14460.84960.07920.23270.64490.07320.366486.042534.914331.9383
301.26680.07880.19011.5501-0.47540.18450.0278-0.1731-0.44940.3244-0.01330.40560.1454-0.1666-0.03960.8947-0.1420.11840.08270.01480.324493.26137.779519.7391
313.3545-0.0456-1.18672.373-0.90763.62920.04460.1576-0.69530.1420.05690.84280.4295-0.8772-0.10260.7147-0.1943-0.03810.7197-0.07350.934183.83473.148611.6531
321.7021-0.4573-0.05391.9486-0.14291.67960.03190.0255-0.2387-0.03870.0130.44360.1535-0.4429-0.03420.8002-0.05430.0980.18110.04260.23889.702919.680512.7596
331.7402-0.9539-1.73816.3656-0.63344.50430.0103-0.48830.16980.1398-0.10080.11040.2296-0.27130.07780.56840.02040.20670.2093-0.0080.313995.226924.506124.7485
341.3889-0.6144-0.30513.03290.36520.6187-0.0029-0.22010.02140.6501-0.06280.3124-0.0493-0.19010.03071.0304-0.01510.18690.30030.01210.305893.429925.750629.264
351.00931.81550.12914.9530.29420.0195-0.11980.17320.1065-0.48390.1254-0.4181-0.27650.1256-0.00541.0212-0.0610.11780.10530.01850.4395112.8751.804914.1403
361.134-0.3638-0.37970.63860.02390.8769-0.03380.05010.04050.0485-0.0083-0.08490.07610.0833-0.04191.0516-0.00240.0455-0.0042-0.02270.2062120.175611.5110.2218
370.3189-0.17970.13410.8327-0.05220.80640.0487-0.06040.06990.1505-0.01-0.0678-0.04720.0703-0.00391.122-0.01840.0346-0.09330.04130.2188117.740222.853816.8829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 101 )A22 - 101
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 296 )A102 - 296
3X-RAY DIFFRACTION3chain 'B' and (resid 330 through 397 )B330 - 397
4X-RAY DIFFRACTION4chain 'B' and (resid 398 through 497 )B398 - 497
5X-RAY DIFFRACTION5chain 'B' and (resid 498 through 638 )B498 - 638
6X-RAY DIFFRACTION6chain 'C' and (resid 22 through 41 )C22 - 41
7X-RAY DIFFRACTION7chain 'C' and (resid 42 through 101 )C42 - 101
8X-RAY DIFFRACTION8chain 'C' and (resid 102 through 239 )C102 - 239
9X-RAY DIFFRACTION9chain 'C' and (resid 240 through 296 )C240 - 296
10X-RAY DIFFRACTION10chain 'D' and (resid 330 through 355 )D330 - 355
11X-RAY DIFFRACTION11chain 'D' and (resid 356 through 377 )D356 - 377
12X-RAY DIFFRACTION12chain 'D' and (resid 378 through 397 )D378 - 397
13X-RAY DIFFRACTION13chain 'D' and (resid 398 through 414 )D398 - 414
14X-RAY DIFFRACTION14chain 'D' and (resid 415 through 572 )D415 - 572
15X-RAY DIFFRACTION15chain 'D' and (resid 573 through 638 )D573 - 638
16X-RAY DIFFRACTION16chain 'E' and (resid 22 through 42 )E22 - 42
17X-RAY DIFFRACTION17chain 'E' and (resid 43 through 101 )E43 - 101
18X-RAY DIFFRACTION18chain 'E' and (resid 102 through 167 )E102 - 167
19X-RAY DIFFRACTION19chain 'E' and (resid 168 through 181 )E168 - 181
20X-RAY DIFFRACTION20chain 'E' and (resid 182 through 239 )E182 - 239
21X-RAY DIFFRACTION21chain 'E' and (resid 240 through 296 )E240 - 296
22X-RAY DIFFRACTION22chain 'F' and (resid 330 through 351 )F330 - 351
23X-RAY DIFFRACTION23chain 'F' and (resid 352 through 397 )F352 - 397
24X-RAY DIFFRACTION24chain 'F' and (resid 398 through 460 )F398 - 460
25X-RAY DIFFRACTION25chain 'F' and (resid 461 through 490 )F461 - 490
26X-RAY DIFFRACTION26chain 'F' and (resid 491 through 638 )F491 - 638
27X-RAY DIFFRACTION27chain 'G' and (resid 22 through 42 )G22 - 42
28X-RAY DIFFRACTION28chain 'G' and (resid 43 through 59 )G43 - 59
29X-RAY DIFFRACTION29chain 'G' and (resid 60 through 101 )G60 - 101
30X-RAY DIFFRACTION30chain 'G' and (resid 102 through 167 )G102 - 167
31X-RAY DIFFRACTION31chain 'G' and (resid 168 through 181 )G168 - 181
32X-RAY DIFFRACTION32chain 'G' and (resid 182 through 239 )G182 - 239
33X-RAY DIFFRACTION33chain 'G' and (resid 240 through 256 )G240 - 256
34X-RAY DIFFRACTION34chain 'G' and (resid 257 through 296 )G257 - 296
35X-RAY DIFFRACTION35chain 'H' and (resid 330 through 397 )H330 - 397
36X-RAY DIFFRACTION36chain 'H' and (resid 398 through 497 )H398 - 497
37X-RAY DIFFRACTION37chain 'H' and (resid 498 through 638 )H498 - 638

+
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