[English] 日本語
Yorodumi
- PDB-8ql1: Crystal structure of the human MDN1-MIDAS/NLE1-UBL complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ql1
TitleCrystal structure of the human MDN1-MIDAS/NLE1-UBL complex
Components
  • NDE1
  • Notchless protein homolog 1
KeywordsRIBOSOME / AAA+ ATPase / Metal ion dependent adhesion site (MIDAS) / Ubiquitin-like domain (Ubl) / pre-60S biogenesis
Function / homology
Function and homology information


hematopoietic stem cell homeostasis / inner cell mass cell differentiation / regulation of Notch signaling pathway / skeletal system morphogenesis / negative regulation of mitotic cell cycle / somitogenesis / Notch signaling pathway / ribosomal large subunit biogenesis / kidney development / positive regulation of canonical Wnt signaling pathway ...hematopoietic stem cell homeostasis / inner cell mass cell differentiation / regulation of Notch signaling pathway / skeletal system morphogenesis / negative regulation of mitotic cell cycle / somitogenesis / Notch signaling pathway / ribosomal large subunit biogenesis / kidney development / positive regulation of canonical Wnt signaling pathway / mitotic cell cycle / nucleolus / nucleoplasm
Similarity search - Function
NLE / NLE (NUC135) domain / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...NLE / NLE (NUC135) domain / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Notchless protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWild, K. / Fiorentino, F. / Hurt, E. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits.
Authors: Federica Fiorentino / Matthias Thoms / Klemens Wild / Timo Denk / Jingdong Cheng / Jakub Zeman / Irmgard Sinning / Ed Hurt / Roland Beckmann /
Abstract: The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ...The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ribosome biogenesis between yeast and humans, illustrated by the structural similarities of ribosomal subunit intermediates. By using X-ray crystallography and cryo-EM, the interaction between the human AAA+ ATPase MDN1 and the 60S assembly factor NLE1 is compared with the yeast homologs Rea1 and Rsa4. The MDN1-MIDAS and NLE1-Ubl complex structure at 2.3 Å resolution mirrors the highly conserved interaction patterns observed in yeast. Moreover, human pre-60S intermediates bound to the dominant negative NLE1-E85A mutant revealed at 2.8 Å resolution an architecture that largely matched the equivalent yeast structures. Conformation of rRNA, assembly factors and their interaction networks are highly conserved. Additionally, novel human pre-60S intermediates with a non-rotated 5S RNP and processed ITS2/foot structure but incomplete intersubunit surface were identified to be similar to counterparts observed in yeast. These findings confirm that the MDN1-NLE1-driven transition phase of the 60S assembly is essentially identical, supporting the idea that ribosome biogenesis is a highly conserved process across eukaryotic cells, employing an evolutionary preservation of ribosomal assembly mechanisms.
History
DepositionSep 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NDE1
B: Notchless protein homolog 1
C: NDE1
D: Notchless protein homolog 1
E: NDE1
F: Notchless protein homolog 1
G: NDE1
H: Notchless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,47712
Polymers172,3808
Non-polymers974
Water7,476415
1
A: NDE1
B: Notchless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1193
Polymers43,0952
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-23 kcal/mol
Surface area16620 Å2
2
C: NDE1
D: Notchless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1193
Polymers43,0952
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-23 kcal/mol
Surface area15620 Å2
3
E: NDE1
F: Notchless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1193
Polymers43,0952
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-22 kcal/mol
Surface area15660 Å2
4
G: NDE1
H: Notchless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1193
Polymers43,0952
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-24 kcal/mol
Surface area16100 Å2
Unit cell
Length a, b, c (Å)237.160, 69.818, 103.183
Angle α, β, γ (deg.)90.00, 91.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-223-

HOH

-
Components

#1: Protein
NDE1


Mass: 31597.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein
Notchless protein homolog 1


Mass: 11496.986 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLE1, HUSSY-07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVX2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 18.2% v/v Polyethylene glycol 300, 0.1 M Sodium Acetate, 3.5 M Ammonium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9625 Å / Relative weight: 1
ReflectionResolution: 2.3→118.522 Å / Num. obs: 75310 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.981 / Rpim(I) all: 0.074 / Net I/σ(I): 8.9
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 7442 / CC1/2: 0.675

-
Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→118.52 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 3805 5.07 %0
Rwork0.2144 ---
obs0.2161 75008 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→118.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10351 0 4 415 10770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310537
X-RAY DIFFRACTIONf_angle_d0.55814283
X-RAY DIFFRACTIONf_dihedral_angle_d15.0743921
X-RAY DIFFRACTIONf_chiral_restr0.0431662
X-RAY DIFFRACTIONf_plane_restr0.0041854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.40191510.35122616X-RAY DIFFRACTION100
2.33-2.360.33821360.32322580X-RAY DIFFRACTION100
2.36-2.390.35031460.31032654X-RAY DIFFRACTION100
2.39-2.430.34661410.29322607X-RAY DIFFRACTION100
2.43-2.460.33261280.28162613X-RAY DIFFRACTION100
2.46-2.50.29381250.26552640X-RAY DIFFRACTION100
2.5-2.540.25111200.25622674X-RAY DIFFRACTION100
2.54-2.590.2951260.25292653X-RAY DIFFRACTION99
2.59-2.630.321490.25792599X-RAY DIFFRACTION100
2.63-2.680.3241370.26692643X-RAY DIFFRACTION100
2.68-2.740.29441330.2752599X-RAY DIFFRACTION100
2.74-2.80.30621180.26862672X-RAY DIFFRACTION100
2.8-2.860.34221410.27632628X-RAY DIFFRACTION100
2.86-2.930.31561280.25722662X-RAY DIFFRACTION100
2.93-3.010.27741600.24412604X-RAY DIFFRACTION100
3.01-3.10.25381380.22662649X-RAY DIFFRACTION100
3.1-3.20.27031340.22572654X-RAY DIFFRACTION100
3.2-3.320.25521430.23352622X-RAY DIFFRACTION100
3.32-3.450.26251710.22892613X-RAY DIFFRACTION100
3.45-3.610.25581460.20872639X-RAY DIFFRACTION100
3.61-3.80.23871290.21062624X-RAY DIFFRACTION99
3.8-4.040.19451450.18372652X-RAY DIFFRACTION100
4.04-4.350.19061530.15562663X-RAY DIFFRACTION100
4.35-4.780.18771280.14842669X-RAY DIFFRACTION100
4.78-5.480.20511840.16642614X-RAY DIFFRACTION100
5.48-6.90.22921650.19382677X-RAY DIFFRACTION99
6.9-118.520.1891300.17612683X-RAY DIFFRACTION96
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)
10.5718-0.69820.54241.2879-1.34681.6770.0096-0.06910.8457-0.32150.4117-1.0924-0.71260.31-0.22030.5153-0.04960.21370.4013-0.08240.974590.165940.918381.4158
25.45620.0044-1.11911.5728-0.90813.00260.18450.13160.4476-0.1717-0.0364-0.26790.02940.0575-0.24440.3569-0.0160.04970.2347-0.00440.453480.710636.633480.7273
33.06940.3124-0.78222.24090.3474.27820.04810.25340.6568-0.44490.1364-0.7304-0.55150.1527-0.20620.4888-0.02580.15220.31880.06220.62876.546144.430276.4872
42.26980.0114-1.10361.65080.61745.93290.05010.39320.0684-0.30230.0868-0.2609-0.1243-0.07170.02880.39060.00040.06470.40670.02760.478267.30635.284371.043
52.7329-0.03150.41692.50780.61514.0854-0.08790.1907-0.0960.002-0.18630.13040.0296-0.36480.02730.2981-0.01360.06630.2371-0.00550.34370.100833.089778.5716
64.36311.1804-4.92943.2022-0.42465.8536-0.4748-0.0961-1.08040.2647-0.39640.07951.16120.41920.89630.3687-0.0032-0.04250.4235-0.00540.318361.30826.983777.9877
75.6129-0.18420.94962.1308-1.36591.0115-0.0232-0.66330.23620.20940.02880.05-0.04340.3676-0.12090.2715-0.05110.06920.2846-0.08720.383673.486930.61390.4679
84.9905-0.0146-1.61321.85421.41014.2501-0.3775-0.1022-0.79270.0375-0.07920.23040.4689-0.61060.37660.3210.01090.05310.3170.00220.356564.006623.838994.6598
94.7341-0.97352.271.2997-0.04918.41830.19970.3526-0.2926-0.1649-0.2688-0.11160.98660.0776-0.13120.42520.020.12060.3098-0.04090.434783.513623.637479.6897
105.7418-1.18720.8734.9891-0.11641.6123-0.132-0.50040.29460.2808-0.1583-0.00640.4493-0.7940.33340.2398-0.0020.07230.3635-0.07040.394158.723134.528101.7912
115.0588-2.8365-0.31196.00520.49312.9097-0.213-0.16-0.35320.56420.13740.3506-0.03680.19560.15390.27890.0030.07240.3041-0.0490.330651.695931.7911106.9792
126.7563-0.8534-4.4653.22540.73416.70630.149-0.27110.42560.1630.18220.2512-0.22140.1146-0.30670.26540.00810.02920.243-0.04240.337951.510840.5738105.888
131.4310.5503-0.49912.30590.03852.40670.0039-0.5707-0.03740.3065-0.0737-0.32040.05060.12250.08780.30680.01730.03650.3230.00630.375186.682113.1083101.3308
143.0952-0.68590.82092.06690.27762.9771-0.088-0.5443-0.79270.0468-0.0187-0.18590.55280.0470.16810.44710.0470.11340.37980.07060.696792.35533.351995.8191
154.1599-0.1946-0.92371.85060.21042.0402-0.04590.2496-0.0135-0.40460.1243-0.54310.01360.2261-0.05160.3918-0.00690.15350.3284-0.04220.499994.129215.32281.9851
160.0231-0.2096-0.23322.16483.44357.3109-0.08370.3699-0.0177-0.2576-0.0743-0.7339-0.00930.3173-0.03750.3552-0.02180.23950.523-0.14760.9466112.161212.596980.1884
174.96660.26382.17750.9739-0.20484.1181-0.14660.61181.04440.40180.0775-2.0328-0.35860.9879-0.03430.5353-0.10130.28980.6296-0.07421.6008118.489826.227984.2268
187.44051.4714-0.08621.4261.41762.5365-0.27940.8540.6664-0.6168-0.2363-0.5886-0.5180.4145-0.97410.3958-0.0890.86550.6964-0.02641.5769119.275120.407573.1413
191.06781.26110.7835.7507-1.01276.70610.2251-0.353-0.7303-0.49960.1293-1.69770.120.772-0.29610.57020.13860.2190.7975-0.03361.6341124.10349.313381.4681
201.61791.1254-0.77712.1181-1.1145.1440.4516-1.1253-0.01040.1167-0.282-0.49250.31631.47280.17760.4928-0.00990.28610.7467-0.09571.5191119.699415.524485.4585
211.6602-1.02821.1741.1728-0.69842.96290.1189-0.60730.16520.32350.0189-0.0384-0.1105-0.2904-0.07770.3473-0.08550.060.4249-0.01330.477587.099749.439957.2942
224.27820.10220.34671.1557-0.03642.18660.1235-0.3985-0.20180.0032-0.0923-0.26980.29270.0884-0.03070.33470.02320.04530.25770.04680.406691.622640.634248.6614
235.85360.42170.14360.79710.25992.79190.0935-0.2001-0.4768-0.2204-0.0462-0.6830.19020.2392-0.00740.34620.04090.06430.22750.00490.417695.07941.198638.5984
242.88773.329-1.42968.45581.0115.5015-0.55041.3479-0.2599-0.30680.49190.16480.25680.1392-0.0660.49790.03890.14070.3887-0.07810.61797.843537.122529.2525
253.5713-2.2859-3.42852.52461.30415.66450.3494-0.53110.69890.22820.1082-0.1277-0.21430.5656-0.31110.2414-0.00170.05820.2692-0.00160.402998.637252.139338.894
265.1670.9361-0.45971.4374-0.45991.2974-0.02930.76580.2973-0.23540.0525-0.27590.09250.1268-0.01720.33590.03270.08820.28560.03360.441596.281952.43632.1164
270.2602-0.7125-0.39835.88856.629.2222-0.22640.7627-0.22420.2274-0.09020.26560.5595-0.22920.2650.25930.01640.1270.43130.00430.6046115.151247.508533.0826
283.7567-0.8843-1.72494.69940.8423.39750.05140.3450.6964-0.0970.2791-0.63220.04130.5543-0.09820.3248-0.06070.18310.42690.02410.7398120.259555.18930.0598
295.0361-4.87941.62788.1452-2.02181.92940.34750.19731.5254-0.521-0.479-0.5533-0.6410.02830.13850.5232-0.08280.11260.7317-0.00870.9643127.69360.560426.0375
309.6913-0.1354-0.62417.0849-1.6769.16610.04540.0652-0.9377-0.4483-0.0958-0.841-0.37880.26250.17660.38240.01240.04130.4684-0.04330.6099126.863744.251335.2082
314.68480.0160.37193.2213-0.76313.8307-0.1161-0.1606-0.53880.0207-0.1532-0.78670.19860.55210.10910.2919-0.00610.01350.4811-0.04830.628122.207150.547539.0684
320.41480.92160.47818.52820.3150.9158-0.04040.2830.71890.19220.06340.73-0.5771-0.1688-0.25040.39180.02610.07290.35710.03590.760922.047640.710669.9423
335.51350.2328-0.87962.58830.95521.18540.1314-0.19950.59180.1527-0.12350.4149-0.0370.01130.01420.3861-0.02120.06070.3026-0.05270.45731.802937.37670.3601
343.30610.2478-0.31174.0766-1.19023.2350.1695-0.38380.37030.6039-0.02760.5272-0.3687-0.0205-0.12590.4024-0.0480.08450.3462-0.12450.580238.619540.42575.9513
355.2358-0.34721.88741.05491.54823.3828-0.05610.11370.2120.1139-0.0560.05250.10020.22050.09450.275-0.03060.06740.16920.00350.349843.554129.258567.5407
368.1208-4.05580.27768.4866-0.03778.08410.5870.1895-1.0942-0.5693-0.6322-0.59320.77440.99470.00420.41880.01880.10480.45720.07120.685760.685620.87652.9411
374.68081.7473-0.57012.24060.20612.5045-0.11720.2951-0.0083-0.04850.1878-0.3748-0.04360.2351-0.01330.304-0.04740.04390.25180.03330.407143.29925.077562.2356
383.1166-0.05281.55030.2293-0.49653.43170.0308-0.146-0.11540.3181-0.23940.04170.20770.19360.01090.388-0.01670.10530.2389-0.02180.451828.897623.428373.2743
390.3923-0.5317-0.07710.73320.11840.0303-0.1288-0.09980.390.6004-0.1323-0.4040.03140.070.19840.48170.0003-0.03120.4459-0.05790.522260.759229.397867.1767
405.79510.09331.4961.92220.25377.5407-0.09160.38250.1801-0.0808-0.1959-0.00460.12970.01060.14240.2766-0.05580.03720.30010.04550.40354.144734.830752.9169
410.1647-1.04730.3967.2898-1.31674.1738-0.59161.92260.6153-0.8650.5334-0.2269-0.24980.42290.01120.4221-0.1701-0.07570.80320.220.486451.728436.226942.5885
424.60210.4597-0.0232.67881.03765.6211-0.54460.1189-0.2763-0.2158-0.14110.0485-0.0492-0.01740.65620.3128-0.0760.03070.3224-0.00650.403460.6628.944350.635
433.51851.11730.65312.97234.60018.2503-0.30420.4407-0.131-0.4304-0.10790.45090.29-0.72550.56190.3638-0.0619-0.01260.41440.05810.394863.51734.401344.1322
446.2208-4.2173-4.42629.8311.44783.4950.0716-1.11242.30930.71440.5337-0.8961-0.88910.8766-0.40560.4683-0.09910.04780.6575-0.10.670165.501942.013957.5617
457.16542.387-4.43884.0283-1.9446.64540.5151-0.31092.24680.22740.4529-0.4239-1.03520.2395-1.33410.5690.02010.19710.4908-0.01280.77653.55944.809358.2653
467.31240.2133-5.42031.899-0.56447.37280.34090.6990.8259-0.53090.4648-0.27440.0657-0.3246-0.76860.3325-0.08040.03370.30940.00610.366664.905137.288939.758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5303 through 5335 )
2X-RAY DIFFRACTION2chain 'A' and (resid 5336 through 5418 )
3X-RAY DIFFRACTION3chain 'A' and (resid 5419 through 5462 )
4X-RAY DIFFRACTION4chain 'A' and (resid 5463 through 5478 )
5X-RAY DIFFRACTION5chain 'A' and (resid 5479 through 5505 )
6X-RAY DIFFRACTION6chain 'A' and (resid 5506 through 5518 )
7X-RAY DIFFRACTION7chain 'A' and (resid 5519 through 5540 )
8X-RAY DIFFRACTION8chain 'A' and (resid 5541 through 5571 )
9X-RAY DIFFRACTION9chain 'A' and (resid 5572 through 5591 )
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 32 )
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 72 )
12X-RAY DIFFRACTION12chain 'B' and (resid 73 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 5302 through 5417 )
14X-RAY DIFFRACTION14chain 'C' and (resid 5418 through 5505 )
15X-RAY DIFFRACTION15chain 'C' and (resid 5506 through 5591 )
16X-RAY DIFFRACTION16chain 'D' and (resid 12 through 22 )
17X-RAY DIFFRACTION17chain 'D' and (resid 23 through 32 )
18X-RAY DIFFRACTION18chain 'D' and (resid 33 through 63 )
19X-RAY DIFFRACTION19chain 'D' and (resid 64 through 79 )
20X-RAY DIFFRACTION20chain 'D' and (resid 80 through 95 )
21X-RAY DIFFRACTION21chain 'E' and (resid 5302 through 5335 )
22X-RAY DIFFRACTION22chain 'E' and (resid 5336 through 5477 )
23X-RAY DIFFRACTION23chain 'E' and (resid 5478 through 5505 )
24X-RAY DIFFRACTION24chain 'E' and (resid 5506 through 5518 )
25X-RAY DIFFRACTION25chain 'E' and (resid 5519 through 5540 )
26X-RAY DIFFRACTION26chain 'E' and (resid 5541 through 5591 )
27X-RAY DIFFRACTION27chain 'F' and (resid 12 through 22 )
28X-RAY DIFFRACTION28chain 'F' and (resid 23 through 52 )
29X-RAY DIFFRACTION29chain 'F' and (resid 53 through 63 )
30X-RAY DIFFRACTION30chain 'F' and (resid 64 through 79 )
31X-RAY DIFFRACTION31chain 'F' and (resid 80 through 95 )
32X-RAY DIFFRACTION32chain 'G' and (resid 5303 through 5335 )
33X-RAY DIFFRACTION33chain 'G' and (resid 5336 through 5418 )
34X-RAY DIFFRACTION34chain 'G' and (resid 5419 through 5505 )
35X-RAY DIFFRACTION35chain 'G' and (resid 5506 through 5540 )
36X-RAY DIFFRACTION36chain 'G' and (resid 5541 through 5552 )
37X-RAY DIFFRACTION37chain 'G' and (resid 5553 through 5571 )
38X-RAY DIFFRACTION38chain 'G' and (resid 5572 through 5592 )
39X-RAY DIFFRACTION39chain 'H' and (resid 10 through 15 )
40X-RAY DIFFRACTION40chain 'H' and (resid 16 through 22 )
41X-RAY DIFFRACTION41chain 'H' and (resid 23 through 32 )
42X-RAY DIFFRACTION42chain 'H' and (resid 33 through 52 )
43X-RAY DIFFRACTION43chain 'H' and (resid 53 through 72 )
44X-RAY DIFFRACTION44chain 'H' and (resid 73 through 79 )
45X-RAY DIFFRACTION45chain 'H' and (resid 80 through 87 )
46X-RAY DIFFRACTION46chain 'H' and (resid 88 through 99 )

+
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