[English] 日本語
Yorodumi
- PDB-9e3t: RTA-RUNT-165 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e3t
TitleRTA-RUNT-165 complex
ComponentsRicin A chain
KeywordsTOXIN / HYDROLASE/INHIBITOR / N-linked glycosidase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil ...Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRudolph, M.J. / Tumer, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072425 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Binding of small molecules at the P-stalk site of ricin A subunit trigger conformational changes that extend into the active site.
Authors: McLaughlin, J.E. / Rudolph, M.J. / Dutta, A. / Li, X.P. / Tsymbal, A.M. / Chen, Y. / Bhattacharya, S. / Algava, B. / Goger, M. / Roberge, J.Y. / Tumer, N.E.
History
DepositionOct 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ricin A chain
B: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2095
Polymers60,6802
Non-polymers5283
Water9,746541
1
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6223
Polymers30,3401
Non-polymers2822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5872
Polymers30,3401
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.858, 57.467, 124.908
Angle α, β, γ (deg.)90.000, 94.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Ricin A chain


Mass: 30340.205 Da / Num. of mol.: 2 / Fragment: residues 40-294
Source method: isolated from a genetically manipulated source
Details: Ricin toxin catalytic subunit, N-linked glycosidase
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli B (bacteria) / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-A1BH4 / (5M)-5-(2-ethyl-6-methylphenyl)thiophene-2-carboxylic acid


Mass: 246.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM Hepes pH 6.5 and 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 85134 / % possible obs: 95.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.29 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.16 / Net I/σ(I): 1.1
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 4320 / CC1/2: 0.45

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.24 Å / SU ML: 0.2154 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.4623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 2393 5.01 %
Rwork0.1923 45330 -
obs0.1943 47723 93.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 35 541 4679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364236
X-RAY DIFFRACTIONf_angle_d0.59055766
X-RAY DIFFRACTIONf_chiral_restr0.0433639
X-RAY DIFFRACTIONf_plane_restr0.0063761
X-RAY DIFFRACTIONf_dihedral_angle_d14.38841549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30031050.25372160X-RAY DIFFRACTION76.34
1.84-1.880.31711320.24562656X-RAY DIFFRACTION94.13
1.88-1.920.30711380.23322486X-RAY DIFFRACTION88.14
1.92-1.970.28581430.22112513X-RAY DIFFRACTION89.25
1.97-2.030.25521420.20182781X-RAY DIFFRACTION98.55
2.03-2.090.25321310.20172762X-RAY DIFFRACTION98.33
2.09-2.150.22961590.1932794X-RAY DIFFRACTION97.98
2.15-2.230.23611200.19032764X-RAY DIFFRACTION97.8
2.23-2.320.2621440.18842781X-RAY DIFFRACTION98.29
2.32-2.420.24371370.19772767X-RAY DIFFRACTION97.03
2.42-2.550.261460.20332715X-RAY DIFFRACTION96.36
2.55-2.710.22371590.19512537X-RAY DIFFRACTION91.02
2.71-2.920.23351400.19522565X-RAY DIFFRACTION90.5
2.92-3.220.21511490.18422794X-RAY DIFFRACTION97.68
3.22-3.680.19811420.17852772X-RAY DIFFRACTION97.36
3.68-4.640.18461450.15832733X-RAY DIFFRACTION94.98
4.64-42.240.23661610.19442750X-RAY DIFFRACTION93.99
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)
11.68545941852-0.02927769021090.2015982285891.825377377250.08198738510541.267673059210.02249195756980.0892816302201-0.07968945299610.120346610681-0.05814781565320.0891775721490.178521897694-0.05549970180720.03422302641680.140540688812-0.0480612310676-0.002177298430370.120174849138-0.02367537610140.1534781829446.10128100066-8.1360732576447.8934393265
21.56294469317-0.385253558933-0.3634386996050.9587994775890.05148208484052.104444874760.05435930543190.1977407293970.027522233873-0.1280031985410.03932104294340.0587580419103-0.0875142282406-0.388615581912-0.1286137383480.127013356998-0.0120169046247-0.02207730927440.126792216478-0.0004575747108390.1371469789546.668926159640.60300266993743.2417731059
31.079939259570.4482173456131.479806023771.949022694020.6632638544932.27413982687-0.01473479348250.01008552749330.196145568163-0.06341976088020.04698026710280.187365434675-0.211064247628-0.158750362975-0.03818329971220.09536695088870.02127636020030.02187443544750.0847824121886-0.00318864483510.11749424998510.319656056710.446249933353.0206059117
42.017940914270.00841026045042-0.7075883193272.459040231270.3428412408141.640902752540.0367563703238-0.1403002569150.008662954086270.3037715082870.0157928250272-0.1426553515050.000886398067090.100111998767-0.06880095431470.0944399593166-0.00234094523461-0.02308083121090.1308006385510.01092925348310.099653318758822.5306287678-1.1233377715857.0287203281
50.967740550911-0.0376871051947-0.1201559827261.318815266490.2723499969231.834190924040.00961592951583-0.0217328696057-0.0719783622460.0229488351042-0.0113446357854-0.009660174155510.3477707050440.01108623659920.0007726918210730.120160152522-0.0124219259937-0.007344906736280.1025399759280.00493165823280.098548020379520.8947597029-8.8857284618848.1128419439
61.49822767333-0.7165414384570.8887271739751.175143548520.0669489504172.30678858630.04866408400730.06975263956610.0825965813405-0.242299989802-0.0381429115517-0.0835443414684-0.2510018436220.240222696599-0.01042941294520.155092295998-0.02133550280.01478101186240.129930228294-0.001155339619440.099876357024625.060606566-2.9878611726729.5208271149
72.11403420504-0.0441463794552-0.006157378555912.57365739628-0.3956271802222.325509886770.0133563757640.242366270488-0.0142438249266-0.6069255282820.1382998890720.217755680242-0.134253674336-0.224485004857-0.1825203155110.239064698135-0.0102593783608-0.004694855250930.165327736165-0.0002278744651260.081550114760413.3406537224-0.015029585142330.2528899805
81.098640056190.230558706254-0.09883888039961.13914495486-0.4103449750231.625654291460.0155359543304-0.02086548278410.01305470405560.0610589936079-0.03299960986110.120331006292-0.273594012387-0.1364821685480.0006851944310070.09255198772040.03031181817310.006622419918650.0707665295638-0.007407003142030.10982487535810.4857433133-21.7975832314.4764221002
91.458110292280.2146534558840.1314484960921.26211280050.04204236717531.812875899250.026523743621-0.2204686964740.02165255538320.0838714603057-0.02754270634830.05616807419070.100903668721-0.223984646671-0.02067306194490.09394955981010.01972510007490.01661700846150.111656934724-0.005669293178170.10892025959911.1538806147-30.862003612719.1612410647
101.04704720992-0.260958125687-1.277281354081.860109197480.8888159722242.019343016090.00371772074639-0.0641408402628-0.1026512250570.1307934349660.04878686739850.01673519156710.212754521482-0.0323546228341-0.01298483626250.09412661218350.00663729998549-0.008586256406950.0867163894754-0.003029983254810.096166287931114.9083649033-40.88716732089.56051723614
111.67271812971-0.1628491477470.9280903348772.665373636790.1549959010522.015187595640.001672436191360.0717950538105-0.0675993881413-0.06314273444060.0703457947666-0.217620276847-0.006909614569650.0903154630508-0.05147882229250.07718613916160.0160895602610.02214060772080.108456848545-4.66607840478E-50.087168311091126.9072880308-29.21009918715.36888596187
120.3440956309840.111858812627-0.06332389256680.8067563650390.2942871741542.056626835620.0466622285778-0.0714478947548-0.02848082464460.106720079844-0.0311640829503-0.043593165505-0.02949201158420.0449822721416-0.01462252996790.1144934850980.0119499943886-0.01069129107340.1122826612740.01075436128370.086322133250625.4398290385-23.910034982818.4067120187
131.127854871980.5425333850790.1537158282811.022680707320.2201771378231.0474265140.0867255237309-0.283535416197-0.0919827678230.28522945065-0.0623141081469-0.1055599465440.2304335571970.182557172847-0.01905223065570.254340462428-0.0103079175779-0.02502138953710.1966603368830.008699736404290.12738033972326.3683869621-26.561485733334.8847747992
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 32 )AA3 - 321 - 30
22chain 'A' and (resid 33 through 75 )AA33 - 7531 - 73
33chain 'A' and (resid 76 through 122 )AA76 - 12274 - 120
44chain 'A' and (resid 123 through 160 )AA123 - 160121 - 158
55chain 'A' and (resid 161 through 201 )AA161 - 201159 - 199
66chain 'A' and (resid 202 through 248 )AA202 - 248200 - 246
77chain 'A' and (resid 249 through 261 )AA249 - 261247 - 259
88chain 'B' and (resid 4 through 32 )BB4 - 321 - 29
99chain 'B' and (resid 33 through 75 )BB33 - 7530 - 72
1010chain 'B' and (resid 76 through 122 )BB76 - 12273 - 119
1111chain 'B' and (resid 123 through 160 )BB123 - 160120 - 157
1212chain 'B' and (resid 161 through 220 )BB161 - 220158 - 217
1313chain 'B' and (resid 221 through 263 )BB221 - 263218 - 260

+
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