[English] 日本語
Yorodumi
- PDB-7mnp: Crystal Structure of the ZnF2 of Nucleoporin NUP358/RanBP2 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mnp
TitleCrystal Structure of the ZnF2 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
Components
  • E3 SUMO-protein ligase RanBP2
  • GTP-binding nuclear protein Ran
KeywordsTRANSPORT PROTEIN / NUCLEAR PORE COMPLEX COMPONENT / NUCLEOCYTOPLASMIC TRANSPORT / ZINC FINGER
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly / manchette / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Transferases; Acyltransferases; Aminoacyltransferases / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / dynein intermediate chain binding / regulation of gluconeogenesis / DNA metabolic process / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / protein sumoylation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / Regulation of HSF1-mediated heat shock response / mRNA transport / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / response to amphetamine / centriole / protein export from nucleus / viral process / SUMOylation of chromatin organization proteins / GTPase activator activity / mitotic spindle organization / G protein activity / HCMV Late Events / male germ cell nucleus / RHO GTPases Activate Formins / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Signaling by ALK fusions and activated point mutants / recycling endosome / ISG15 antiviral mechanism / small GTPase binding / positive regulation of protein import into nucleus / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / GDP binding / melanosome / protein folding / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / snRNP Assembly / midbody / actin cytoskeleton organization / nuclear membrane / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding
Similarity search - Function
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Zinc finger domain ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Tetratricopeptide-like helical domain superfamily / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / E3 SUMO-protein ligase RanBP2 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsBley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. ...Bley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. / Brown, B. / Tang, A.W. / Rundlet, E.J. / Correia, A.R. / Chen, S. / Regmi, S.G. / Stevens, T.A. / Jette, C.A. / Dasso, M. / Patke, A. / Palazzo, A.F. / Kossiakoff, A.A. / Hoelz, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117360 United States
Howard Hughes Medical Institute (HHMI)55108534 United States
Heritage Medical Research Institute United States
CitationJournal: Science / Year: 2022
Title: Architecture of the cytoplasmic face of the nuclear pore.
Authors: Christopher J Bley / Si Nie / George W Mobbs / Stefan Petrovic / Anna T Gres / Xiaoyu Liu / Somnath Mukherjee / Sho Harvey / Ferdinand M Huber / Daniel H Lin / Bonnie Brown / Aaron W Tang / ...Authors: Christopher J Bley / Si Nie / George W Mobbs / Stefan Petrovic / Anna T Gres / Xiaoyu Liu / Somnath Mukherjee / Sho Harvey / Ferdinand M Huber / Daniel H Lin / Bonnie Brown / Aaron W Tang / Emily J Rundlet / Ana R Correia / Shane Chen / Saroj G Regmi / Taylor A Stevens / Claudia A Jette / Mary Dasso / Alina Patke / Alexander F Palazzo / Anthony A Kossiakoff / André Hoelz /
Abstract: INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are ...INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are generated by the circumscribed fusion of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) are the sole bidirectional gateways for nucleocytoplasmic transport. The ~110-MDa human NPC is an ~1000-protein assembly that comprises multiple copies of ~34 different proteins, collectively termed nucleoporins. The symmetric core of the NPC is composed of an inner ring encircling the central transport channel and outer rings formed by Y‑shaped coat nucleoporin complexes (CNCs) anchored atop both sides of the nuclear envelope. The outer rings are decorated with compartment‑specific asymmetric nuclear basket and cytoplasmic filament nucleoporins, which establish transport directionality and provide docking sites for transport factors and the small guanosine triphosphatase Ran. The cytoplasmic filament nucleoporins also play an essential role in the irreversible remodeling of messenger ribonucleoprotein particles (mRNPs) as they exit the central transport channel. Unsurprisingly, the NPC's cytoplasmic face represents a hotspot for disease‑associated mutations and is commonly targeted by viral virulence factors. RATIONALE Previous studies established a near-atomic composite structure of the human NPC's symmetric core by combining (i) biochemical reconstitution to elucidate the interaction network between symmetric nucleoporins, (ii) crystal and single-particle cryo-electron microscopy structure determination of nucleoporins and nucleoporin complexes to reveal their three-dimensional shape and the molecular details of their interactions, (iii) quantitative docking in cryo-electron tomography (cryo-ET) maps of the intact human NPC to uncover nucleoporin stoichiometry and positioning, and (iv) cell‑based assays to validate the physiological relevance of the biochemical and structural findings. In this work, we extended our approach to the cytoplasmic filament nucleoporins to reveal the near-atomic architecture of the cytoplasmic face of the human NPC. RESULTS Using biochemical reconstitution, we elucidated the protein-protein and protein-RNA interaction networks of the human and cytoplasmic filament nucleoporins, establishing an evolutionarily conserved heterohexameric cytoplasmic filament nucleoporin complex (CFNC) held together by a central heterotrimeric coiled‑coil hub that tethers two separate mRNP‑remodeling complexes. Further biochemical analysis and determination of a series of crystal structures revealed that the metazoan‑specific cytoplasmic filament nucleoporin NUP358 is composed of 16 distinct domains, including an N‑terminal S‑shaped α‑helical solenoid followed by a coiled‑coil oligomerization element, numerous Ran‑interacting domains, an E3 ligase domain, and a C‑terminal prolyl‑isomerase domain. Physiologically validated quantitative docking into cryo-ET maps of the intact human NPC revealed that pentameric NUP358 bundles, conjoined by the oligomerization element, are anchored through their N‑terminal domains to the central stalk regions of the CNC, projecting flexibly attached domains as far as ~600 Å into the cytoplasm. Using cell‑based assays, we demonstrated that NUP358 is dispensable for the architectural integrity of the assembled interphase NPC and RNA export but is required for efficient translation. After NUP358 assignment, the remaining 4-shaped cryo‑ET density matched the dimensions of the CFNC coiled‑coil hub, in close proximity to an outer-ring NUP93. Whereas the N-terminal NUP93 assembly sensor motif anchors the properly assembled related coiled‑coil channel nucleoporin heterotrimer to the inner ring, biochemical reconstitution confirmed that the NUP93 assembly sensor is reused in anchoring the CFNC to the cytoplasmic face of the human NPC. By contrast, two CFNCs are anchored by a divergent mechanism that involves assembly sensors located in unstructured portions of two CNC nucleoporins. Whereas unassigned cryo‑ET density occupies the NUP358 and CFNC binding sites on the nuclear face, docking of the nuclear basket component ELYS established that the equivalent position on the cytoplasmic face is unoccupied, suggesting that mechanisms other than steric competition promote asymmetric distribution of nucleoporins. CONCLUSION We have substantially advanced the biochemical and structural characterization of the asymmetric nucleoporins' architecture and attachment at the cytoplasmic and nuclear faces of the NPC. Our near‑atomic composite structure of the human NPC's cytoplasmic face provides a biochemical and structural framework for elucidating the molecular basis of mRNP remodeling, viral virulence factor interference with NPC function, and the underlying mechanisms of nucleoporin diseases at the cytoplasmic face of the NPC. [Figure: see text].
History
DepositionMay 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,25310
Polymers58,1874
Non-polymers1,0666
Water4,792266
1
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6265
Polymers29,0932
Non-polymers5333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-29 kcal/mol
Surface area11840 Å2
MethodPISA
2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6265
Polymers29,0932
Non-polymers5333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-30 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.230, 79.840, 108.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 24483.086 Da / Num. of mol.: 2 / Mutation: F35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Production host: Escherichia coli (E. coli) / References: UniProt: P62826
#2: Protein/peptide E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270


Mass: 4610.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Production host: Escherichia coli (E. coli) / References: UniProt: P49792

-
Non-polymers , 4 types, 272 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 17 % (w/v) PEG 3,350; 0.1M Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→29.02 Å / Num. obs: 62430 / % possible obs: 99.4 % / Redundancy: 10.9 % / Biso Wilson estimate: 29.62 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.127 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.05-2.139.11.62866931400.4671.46895.3
4.42-29.0310.435.93672935370.0130.04599.7

-
Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.05→29.02 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 3045 4.88 %
Rwork0.1941 59385 -
obs0.196 62430 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.16 Å2 / Biso mean: 50.4632 Å2 / Biso min: 20.84 Å2
Refinement stepCycle: final / Resolution: 2.05→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 84 266 4170
Biso mean--37.34 41.53 -
Num. residues----480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.090.3877950.3972295239083
2.09-2.120.34951460.33432655280199
2.12-2.160.33281460.299127842930100
2.16-2.20.2921270.288127042831100
2.2-2.240.30571550.269627062861100
2.24-2.280.28291430.261327272870100
2.28-2.330.2671430.240927282871100
2.33-2.390.31171590.252927132872100
2.39-2.450.27711200.24127322852100
2.45-2.510.25511490.220927252874100
2.51-2.590.28011350.225827402875100
2.59-2.670.31721430.209326902833100
2.67-2.770.2831130.22352749286299
2.77-2.880.211620.22342699286199
2.88-3.010.26841310.20092700283198
3.01-3.170.23281660.196226822848100
3.17-3.360.15881050.184527732878100
3.36-3.620.22531420.172927312873100
3.62-3.990.16341480.147227332881100
3.99-4.560.1771520.134326852837100
4.56-5.740.22171390.14232686282598
5.74-29.020.21611260.176527482874100
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)
10.1087-0.1174-0.0390.15380.17070.24720.1389-0.7971-0.9950.54370.14760.46640.512-0.0040.00220.40340.0173-0.0060.38270.04650.613523.3165-1.412128.9647
21.46-0.3179-0.58212.83390.2731.3511-0.0302-0.0286-0.0235-0.05730.1156-0.0002-0.03380.071200.2403-0.02170.02650.27090.01410.253613.83165.642424.1185
31.5379-0.0716-1.09571.41960.50671.3017-0.0131-0.16720.3957-0.31810.1312-0.4497-0.6750.097900.5212-0.09430.05740.377-0.0660.505719.772718.588220.7202
41.8072-1.5195-0.79972.26130.35612.36570.16920.33430.1259-0.95060.0549-0.3205-0.62340.24490.02430.5609-0.08980.10330.38730.00870.296116.907412.29348.0733
50.48820.2128-0.38391.5357-0.0590.8578-0.03740.1868-0.2909-0.47620.131-0.3512-0.04630.088800.3587-0.04240.06840.3719-0.02160.422322.5801-1.08914.0748
60.1956-0.305-0.08380.7911-0.13910.33390.21170.17660.377-1.2979-0.3153-0.6648-0.53150.28130.00740.864-0.07040.26480.56940.03370.491520.315710.3072-1.1234
70.04640.00870.04570.0390.03870.06060.7384-0.2682-0.5954-0.8159-0.0627-1.20110.49060.72540.00010.82160.2530.20120.7898-0.09640.972837.1198-11.447821.7463
80.00380.005-0.00580.00570.01510.0241-0.18090.4062-0.2062-0.0618-0.13120.51810.11740.057201.0676-0.2029-0.13521.11480.37611.071931.494-5.923336.7829
90.03020.1272-0.11670.8681-0.76090.7267-0.4044-0.9171-0.855-0.03430.1399-0.48890.74760.5655-0.04460.36970.12250.02380.68170.09330.487721.87571.010140.5795
101.01990.49250.3341.0962-0.20890.27240.2935-0.94770.05880.61380.03490.1766-0.21670.73460.05360.5032-0.0125-0.07210.74540.02020.185316.22715.011343.7536
110.10780.17760.30120.44280.88891.8094-0.14380.69811.4097-0.62970.34260.0428-1.397-0.5418-0.05510.4771-0.00860.09170.4330.18990.550154.871922.217424.7718
121.841-0.47670.331.9774-0.57451.804-0.12540.13850.0237-0.09630.16970.3470.0318-0.273400.29990.02330.02210.2893-0.00210.32544.114216.979230.8319
133.79210.79570.52422.9259-0.19052.11350.0989-0.0295-0.68320.08480.0816-0.0780.34970.02820.00130.36080.02460.00920.28710.03390.463246.06553.118835.2919
141.65241.18010.41160.9477-0.2862.2601-0.0289-0.4187-0.58780.29320.0339-0.19330.31980.10350.00050.4170.0318-0.0090.34970.07280.415752.027710.793941.9232
150.06280.0250.07271.1330.26590.8839-0.3597-0.52720.12890.5470.30610.040.0410.2088-00.39470.05640.01180.3740.02970.412950.482421.772241.6657
160.52230.5620.23770.8747-0.08230.4489-0.1129-0.6649-0.41911.47510.1107-0.51490.9290.19200.87610.0772-0.10640.83610.17950.484950.42857.721255.833
170.0410.0446-0.00520.0308-0.0012-0.00540.69610.09680.82420.81970.2112-1.1036-0.08520.9721-00.6049-0.1977-0.06420.6715-0.00531.008667.200129.496532.589
180.00230.00540.01780.00070.0140.0238-0.9221-0.28740.4095-0.50980.5817-0.1473-0.0364-0.216900.7507-0.2935-0.16981.60080.29411.225861.316924.242317.3022
190.0085-0.00020.04520.1761-0.00150.1505-0.651.0670.3806-0.83160.4348-0.54520.0510.0024-00.5851-0.12750.05470.70830.0680.515549.683818.194915.3365
200.2055-0.04570.0060.3141-0.17550.1501-0.20441.56660.2752-1.06230.018-0.1952-0.70140.638300.7919-0.13930.13991.2708-0.09020.66549.613613.856910.8795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 13 )A7 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 94 )A14 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 120 )A95 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 157 )A121 - 157
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 188 )A158 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 207 )A189 - 207
7X-RAY DIFFRACTION7chain 'B' and (resid 1405 through 1410 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1411 through 1416 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1417 through 1432 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1433 through 1443 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 7 through 11 )C7 - 11
12X-RAY DIFFRACTION12chain 'C' and (resid 12 through 59 )C12 - 59
13X-RAY DIFFRACTION13chain 'C' and (resid 60 through 138 )C60 - 138
14X-RAY DIFFRACTION14chain 'C' and (resid 139 through 168 )C139 - 168
15X-RAY DIFFRACTION15chain 'C' and (resid 169 through 188 )C169 - 188
16X-RAY DIFFRACTION16chain 'C' and (resid 189 through 207 )C189 - 207
17X-RAY DIFFRACTION17chain 'D' and (resid 1405 through 1410 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 1411 through 1416 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 1417 through 1426 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 1427 through 1443 )D0

+
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