[English] 日本語
Yorodumi
- PDB-7mnw: Crystal Structure of Nup358/RanBP2 Ran-binding domain 1 in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mnw
TitleCrystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP
Components
  • E3 SUMO-protein ligase RanBP2
  • GTP-binding nuclear protein Ran
KeywordsTRANSPORT PROTEIN / nuclear pore complex component / nucleocytoplasmic transport / complex (small GTPase-nuclear protein)
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / E3 SUMO-protein ligase RanBP2 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
E: GTP-binding nuclear protein Ran
F: E3 SUMO-protein ligase RanBP2
G: GTP-binding nuclear protein Ran
H: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,33316
Polymers163,1478
Non-polymers2,1868
Water7,242402
1
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3334
Polymers40,7872
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-43 kcal/mol
Surface area16380 Å2
MethodPISA
2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3334
Polymers40,7872
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-41 kcal/mol
Surface area16270 Å2
MethodPISA
3
E: GTP-binding nuclear protein Ran
F: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3334
Polymers40,7872
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-44 kcal/mol
Surface area16460 Å2
MethodPISA
4
G: GTP-binding nuclear protein Ran
H: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3334
Polymers40,7872
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-43 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.370, 137.834, 172.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

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


Mass: 24543.182 Da / Num. of mol.: 4
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
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: 16243.673 Da / Num. of mol.: 4
Fragment: RAN-binding domain 1 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 1171-1306)
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, Transferases; Acyltransferases; Aminoacyltransferases
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG3350, 0.2 M potassium sodium tartrate tetrahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→28.96 Å / Num. obs: 64146 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 36.12 Å2 / Rpim(I) all: 0.082 / Rrim(I) all: 0.306 / Net I/σ(I): 6.7 / Num. measured all: 880269
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.4-2.4914.11.38768962190.752.84798.2
5.16-28.9613.413.98971766870.0340.122100

-
Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RRP

1rrp


Resolution: 2.4→28.96 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 3185 4.97 %
Rwork0.1995 60885 -
obs0.2016 64070 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.76 Å2 / Biso mean: 60.1529 Å2 / Biso min: 22.5 Å2
Refinement stepCycle: final / Resolution: 2.4→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11177 0 180 402 11759
Biso mean--47.35 42.79 -
Num. residues----1379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.440.34041120.28952539265196
2.44-2.470.29081490.289726082757100
2.47-2.510.34261230.283626382761100
2.51-2.560.30351340.279726172751100
2.56-2.60.32761380.267326582796100
2.6-2.650.31461500.252825952745100
2.65-2.710.29981220.24626372759100
2.71-2.770.27541390.248226292768100
2.77-2.830.29551470.260326232770100
2.83-2.90.27731330.245726372770100
2.9-2.980.30141400.237626312771100
2.98-3.070.2881380.223526452783100
3.07-3.170.28681420.223926442786100
3.17-3.280.26111410.21926292770100
3.28-3.410.27361520.217826412793100
3.41-3.570.22521550.19626142769100
3.57-3.750.24121410.188426732814100
3.75-3.990.24231330.175626602793100
3.99-4.30.19231270.15626812808100
4.3-4.730.17211360.138126792815100
4.73-5.410.20281390.14527122851100
5.41-6.80.21151630.181826882851100
6.8-28.960.19341310.18542807293899
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)
12.8840.3705-0.65241.6850.17042.57580.0967-0.01950.0022-0.0368-0.1008-0.3163-0.09050.2888-0.00030.2673-0.06760.00170.34210.05890.3569-5.2952-13.0583-25.3619
22.96010.86170.87791.6106-0.9582.27310.1852-0.1737-0.29480.4685-0.1817-0.4830.49110.50500.4169-0.0052-0.10260.6080.08650.60332.2653-22.8651-19.9286
31.55090.12560.06660.57250.77340.90720.0052-0.1929-0.3637-0.0501-0.0756-0.11080.3315-0.2216-0.00090.358-0.0730.00410.39610.06840.3419-15.2513-22.7837-21.3284
46.20371.3555-1.65511.43870.08490.63880.5082.10021.328-1.2336-0.65781.2188-1.1249-0.6986-0.27771.25810.0553-0.08940.95580.25110.9914-29.807-5.8033-49.6226
50.2045-0.541-0.49582.38672.05721.8208-0.4583-0.1197-1.27760.890.4887-0.69291.49790.92180.07020.73850.00320.11230.548-0.12880.9381-15.4673-26.5552-46.4399
60.1789-0.2079-0.07480.2372-0.06560.12280.214-1.13011.16080.7717-0.5883-0.4822-1.390.9044-0.00730.8227-0.16980.03820.8331-0.01810.5325-15.3345-14.9432-6.2599
70.0253-0.0688-0.0180.1656-0.00050.10060.29890.2708-0.1295-0.09710.45510.37180.9769-1.48770.00070.4617-0.1928-0.04730.7568-0.04270.4705-31.678-19.8083-14.1738
80.46380.15270.46720.9895-0.34970.8133-0.0694-0.2605-0.3214-0.0466-0.1120.18370.137-0.377600.2547-0.0340.030.45490.040.3965-34.5372-25.3993-34.5328
94.41470.1504-0.05293.21510.0443.8063-0.1049-0.30570.0788-0.0836-0.058-0.1982-0.2513-0.0587-0.00010.30550.01660.00120.2984-0.00190.2879-28.3955-17.3762-38.8645
102.52561.3875-0.3872.4641-1.70671.5711-0.0630.19980.1973-0.4085-0.1234-0.1175-0.53860.087-00.30210.032-0.00750.36060.05760.3591-26.8658-15.1519-44.8056
111.0851.010.56612.6025-0.07041.79990.44090.4404-0.3416-0.671-0.44620.4847-0.1619-0.3618-0.00030.29060.0299-0.03620.412-0.04830.3805-34.959-25.1423-47.0558
121.63350.27150.32031.99010.33671.27430.0598-0.30410.2310.1019-0.03720.1556-0.2550.1435-0.00050.28170.05570.07030.4393-0.04910.414610.9117-14.0716-56.8492
134.199-0.0192-0.45752.30150.69882.5954-0.0453-0.0168-0.0017-0.199-0.05780.71840.0218-0.5493-0.00070.33730.0597-0.03960.4462-0.09410.7107-1.955-17.1967-60.934
140.0148-0.04330.030.004-0.02-0.00080.39780.2438-0.1161-0.4163-0.22580.4430.57820.3859-0.00011.11890.1912-0.27681.1061-0.22181.2462-3.9505-26.3786-70.4173
152.8539-0.78630.12541.1998-1.0242.0988-0.1470.1819-0.10310.0082-0.0802-0.06830.2690.3059-0.00150.35360.090.0620.3682-0.03440.411118.0905-20.9714-61.1705
161.806-1.5720.94841.418-1.13511.3108-0.3089-0.7956-0.278-0.3965-0.0484-0.3807-0.3646-0.427700.8248-0.02480.16161.0145-0.17890.734724.0026-14.8522-34.3883
170.40010.4509-0.56471.52060.22511.26250.12920.4152-0.02780.00740.1360.3382-1.00090.2466-0.00010.63110.08910.11440.70030.06670.430820.7745-16.4191-75.9998
181.59011.2640.41971.4628-0.5231.20280.1020.322-0.0575-0.3471-0.0975-0.182-0.4349-0.22990.00010.34660.1082-0.01630.5866-0.12860.451731.4025-23.4766-49.3177
190.03530.0413-0.03020.0515-0.02690.006-0.29770.48150.74460.3865-0.3027-0.1577-1.30680.17350.00060.93410.20540.36150.7762-0.14921.322215.9592-8.0141-36.117
201.26740.60441.21432.5365-0.78453.2301-0.16370.46670.1381-0.2937-0.0991-0.0597-0.2049-0.136-0.00570.31190.01320.01410.5026-0.12030.423731.8692-21.0014-48.5224
213.59550.1230.40032.5733-0.15172.4628-0.11870.03330.14880.0694-0.0037-0.0561-0.3111-0.1003-0.00010.32930.06660.00240.4725-0.14110.450529.1915-17.4041-43.0654
220.8108-1.19180.31712.0846-0.76632.28860.128-0.0373-0.0950.3541-0.1825-0.2748-0.18040.0364-0.00010.29750.01850.02610.4061-0.10930.465936.2727-26.9455-39.0416
232.07180.0586-1.15772.151.78432.2206-0.1174-0.0267-0.37610.8232-0.08730.30570.5805-0.6015-0.12830.6939-0.28520.10980.45290.02670.348113.7391-58.5095-14.7527
242.5099-1.1223-0.87072.31450.21492.0757-0.19060.2058-0.95840.05080.11120.30841.149-0.4597-0.07640.8883-0.35250.08040.4427-0.05260.736514.5207-69.8577-20.5573
250.43460.2139-0.28650.40460.06470.2049-0.53990.3865-1.5010.2976-0.2896-0.90331.06020.1422-0.00071.243-0.0710.06781.0797-0.21621.282929.9373-72.9892-20.0729
262.302-0.19341.3142.5339-0.2741.7815-0.1576-0.0194-0.14280.00920.2625-0.22920.02840.060.00970.4483-0.16610.01530.38470.06450.306921.124-51.0765-18.8546
271.71992.2690.91992.85741.01051.4914-0.10570.53770.01351.1477-0.45390.29070.4098-0.50740.00010.7682-0.05760.09020.98580.08260.560814.1928-45.85697.7141
283.5148-0.458-0.71410.1915-0.07920.3775-0.45380.1611-1.0234-1.228-0.260.44980.9531-0.26-0.07651.1217-0.25880.02350.9094-0.12210.548214.9533-55.5544-36.5624
29-0.01950.07310.46570.05220.5113.475-0.16770.39360.373-0.45240.13890.542-2.57450.59120.03620.6039-0.1428-0.02510.59960.01340.511120.5281-37.5906-25.9541
302.3728-1.73090.83062.04910.31723.675-0.0444-0.3385-0.096-0.4528-0.1620.10550.3113-0.1402-0.00090.3964-0.03460.04850.3324-0.04130.299320.8748-42.035-3
312.78460.90010.14422.0258-0.84032.0208-0.20370.08110.1191-0.601-0.04840.02810.0098-0.0281-0.00010.44650.0420.00210.36270.03780.320919.0476-35.5978-6.8626
321.87021.1918-1.56061.53180.12972.8308-0.0838-0.5191-0.43760.1243-0.0790.01190.3629-0.4587-0.00010.3636-0.02190.03370.3443-0.00560.315119.036-41.86582.4683
331.08430.4811-0.06730.5021-0.31330.6461-0.5273-0.4840.93350.73970.2787-0.4257-0.4159-0.573-0.00240.45580.0512-0.01280.4034-0.0650.382924.2568-29.65543.1034
342.5122-0.8064-0.55663.5247-0.05171.6604-0.07-0.12670.28850.79910.0457-0.264-0.01570.26190.00060.5427-0.0888-0.01860.358-0.01630.36957.4199-7.8281-16.5354
351.7237-0.53791.49242.76040.48612.1590.01850.09660.42430.2336-0.1830.3994-0.4753-0.2856-00.6402-0.01650.08570.3357-0.02070.657846.99492.5534-18.8263
361.52140.79390.76742.04051.09660.9610.07590.22790.2888-0.0633-0.14991.019-0.1574-0.4822-0.00220.5295-0.04390.15510.4673-0.03080.656343.6066-7.27-22.659
371.37240.3986-1.19981.78650.30331.3926-0.6034-1.2257-0.08630.6560.1848-0.50220.6816-0.7420.01650.9628-0.02540.1920.55630.01780.72356.7836-31.525-9.8093
380.55680.7168-0.83961.4366-0.46131.90110.22420.5878-1.0691.2716-0.49380.37470.37830.1604-0.00010.8649-0.1085-0.11531.0108-0.15280.878452.3251-21.59248.668
390.5042-0.28930.38530.70920.57340.9237-0.04290.31760.21910.32240.45580.1348-0.22530.2386-0.00010.7392-0.0260.12730.5422-0.03230.443553.0731-21.9918-33.2683
401.2160.66260.09020.6144-0.62030.9703-0.17570.3778-0.4014-1.4215-0.1459-0.04680.1223-0.2099-0.00440.8619-0.055-0.0220.39950.0040.465844.1107-35.4307-9.0479
412.2692-0.8836-1.43311.9199-0.7032.4705-0.3067-0.13240.1019-1.03260.1117-0.4753-0.01740.3394-0.00450.71420.02650.08650.40080.01750.456651.4137-28.5723-2.6222
421.77910.46740.60483.8722-1.03762.04910.0221-0.1303-0.15-0.5305-0.3524-0.7785-0.04050.3942-00.5101-0.00180.03710.46320.04280.465352.6284-28.9243-0.5026
430.20210.0942-0.08990.6511-0.61621.1240.0609-0.2970.8137-0.1978-0.2210.1328-0.4844-0.0449-0.00010.49290.03280.00620.3972-0.05520.411242.2926-26.44614.6335
442.2959-0.7838-0.56271.10260.27941.165-0.451-0.2295-1.34390.52040.26640.69971.46920.2905-0.03320.61460.09710.02490.41480.04840.387946.1829-40.53573.8982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 102 )A7 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 144 )A103 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 184 )A145 - 184
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 207 )A185 - 207
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 216 )A208 - 216
6X-RAY DIFFRACTION6chain 'B' and (resid 1172 through 1179 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1180 through 1185 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1186 through 1200 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1201 through 1253 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1254 through 1283 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1284 through 1306 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 8 through 61 )C8 - 61
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 135 )C62 - 135
14X-RAY DIFFRACTION14chain 'C' and (resid 136 through 144 )C136 - 144
15X-RAY DIFFRACTION15chain 'C' and (resid 145 through 190 )C145 - 190
16X-RAY DIFFRACTION16chain 'C' and (resid 191 through 216 )C191 - 216
17X-RAY DIFFRACTION17chain 'D' and (resid 1172 through 1184 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 1185 through 1205 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 1206 through 1209 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 1210 through 1236 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 1237 through 1283 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 1284 through 1306 )D0
23X-RAY DIFFRACTION23chain 'E' and (resid 7 through 58 )E7 - 58
24X-RAY DIFFRACTION24chain 'E' and (resid 59 through 125 )E59 - 125
25X-RAY DIFFRACTION25chain 'E' and (resid 126 through 144 )E126 - 144
26X-RAY DIFFRACTION26chain 'E' and (resid 145 through 190 )E145 - 190
27X-RAY DIFFRACTION27chain 'E' and (resid 191 through 216 )E191 - 216
28X-RAY DIFFRACTION28chain 'F' and (resid 1172 through 1178 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 1179 through 1188 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 1189 through 1223 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 1224 through 1253 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 1254 through 1289 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 1290 through 1306 )F0
34X-RAY DIFFRACTION34chain 'G' and (resid 7 through 88 )G7 - 88
35X-RAY DIFFRACTION35chain 'G' and (resid 89 through 132 )G89 - 132
36X-RAY DIFFRACTION36chain 'G' and (resid 133 through 171 )G133 - 171
37X-RAY DIFFRACTION37chain 'G' and (resid 172 through 195 )G172 - 195
38X-RAY DIFFRACTION38chain 'G' and (resid 196 through 216 )G196 - 216
39X-RAY DIFFRACTION39chain 'H' and (resid 1172 through 1184 )H0
40X-RAY DIFFRACTION40chain 'H' and (resid 1185 through 1200 )H0
41X-RAY DIFFRACTION41chain 'H' and (resid 1201 through 1235 )H0
42X-RAY DIFFRACTION42chain 'H' and (resid 1236 through 1279 )H0
43X-RAY DIFFRACTION43chain 'H' and (resid 1280 through 1290 )H0
44X-RAY DIFFRACTION44chain 'H' and (resid 1291 through 1306 )H0

+
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