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- PDB-1rrp: STRUCTURE OF THE RAN-GPPNHP-RANBD1 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1rrp
TitleSTRUCTURE OF THE RAN-GPPNHP-RANBD1 COMPLEX
Components
  • NUCLEAR PORE COMPLEX PROTEIN NUP358
  • RAN
KeywordsCOMPLEX (SMALL GTPASE/NUCLEAR PROTEIN) / COMPLEX (SMALL GTPASE-NUCLEAR PROTEIN) / SMALL GTPASE / NUCLEAR TRANSPORT / COMPLEX (SMALL GTPASE-NUCLEAR PROTEIN) complex
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / nuclear pore cytoplasmic filaments / snRNA import into nucleus / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / nuclear pore cytoplasmic filaments / snRNA import into nucleus / Nuclear Pore Complex (NPC) Disassembly / 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 / 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 / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / nuclear export / NLS-bearing protein import into nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMO transferase activity / nucleocytoplasmic transport / centrosome localization / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / regulation of gluconeogenesis / DNA metabolic process / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / protein sumoylation / ribosomal large subunit export from nucleus / mRNA transport / Regulation of HSF1-mediated heat shock response / viral process / ribosomal subunit export from nucleus / nuclear pore / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ribosomal small subunit export from nucleus / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / response to amphetamine / mitotic spindle organization / protein export from nucleus / SUMOylation of chromatin organization proteins / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / ISG15 antiviral mechanism / HCMV Early Events / positive regulation of protein import into nucleus / protein import into nucleus / Separation of Sister Chromatids / GDP binding / Signaling by ALK fusions and activated point mutants / nuclear envelope / melanosome / positive regulation of protein binding / mitotic cell cycle / protein folding / G protein activity / snRNP Assembly / midbody / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / protein-containing complex binding / nucleolus / GTP binding / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus
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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / 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 / PH-domain like / 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 / Small GTP-binding protein domain / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
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: 2.96 Å
AuthorsVetter, I.R. / Nowak, C. / Nishimoto, T. / Kuhlmann, J. / Wittinghofer, A.
Citation
Journal: Nature / Year: 1999
Title: Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport.
Authors: Vetter, I.R. / Nowak, C. / Nishimoto, T. / Kuhlmann, J. / Wittinghofer, A.
#1: Journal: FEBS Lett. / Year: 1997
Title: Ranbp1 is Crucial for the Release of Rangtp from Importin Beta-Related Nuclear Transport Factors
Authors: Bischoff, F.R. / Gorlich, D.
#2: Journal: Biochemistry / Year: 1997
Title: Dynamic and Equilibrium Studies on the Interaction of Ran with its Effector, Ranbp1
Authors: Kuhlmann, J. / Macara, I. / Wittinghofer, A.
#3: Journal: Trends Cell Biol. / Year: 1995
Title: A Ran-Binding Motif Found in Nuclear Pore Proteins
Authors: Hartmann, E. / Gorlich, D.
#4: Journal: Nature / Year: 1995
Title: A Giant Nucleopore Protein that Binds Ran/Tc4
Authors: Yokoyama, N. / Hayashi, N. / Seki, T. / Pante, N. / Ohba, T. / Nishii, K. / Kuma, K. / Hayashida, T. / Miyata, T. / Aebi, U. / Fukui, M. / Nishimoto, T.
#5: Journal: J.Biol.Chem. / Year: 1995
Title: The C Terminus of the Nuclear Ran/Tc4 Gtpase Stabilizes the Gdp-Bound State and Mediates Interactions with Rcc1, Ran-Gap, and Htf9A/Ranbp1
Authors: Richards, S.A. / Lounsbury, K.M. / Macara, I.G.
#6: Journal: Embo J. / Year: 1995
Title: Co-Activation of Rangtpase and Inhibition of GTP Dissociation by Ran-GTP Binding Protein Ranbp1
Authors: Bischoff, F.R. / Krebber, H. / Smirnova, E. / Dong, W. / Ponstingl, H.
History
DepositionJan 15, 1999Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAN
B: NUCLEAR PORE COMPLEX PROTEIN NUP358
C: RAN
D: NUCLEAR PORE COMPLEX PROTEIN NUP358
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8678
Polymers77,7744
Non-polymers1,0934
Water64936
1
A: RAN
B: NUCLEAR PORE COMPLEX PROTEIN NUP358
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4334
Polymers38,8872
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area16180 Å2
MethodPISA
2
C: RAN
D: NUCLEAR PORE COMPLEX PROTEIN NUP358
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4334
Polymers38,8872
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-28 kcal/mol
Surface area15200 Å2
MethodPISA
3
A: RAN
B: NUCLEAR PORE COMPLEX PROTEIN NUP358
C: RAN
D: NUCLEAR PORE COMPLEX PROTEIN NUP358
hetero molecules

A: RAN
B: NUCLEAR PORE COMPLEX PROTEIN NUP358
C: RAN
D: NUCLEAR PORE COMPLEX PROTEIN NUP358
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,73316
Polymers155,5478
Non-polymers2,1868
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area25430 Å2
ΔGint-150 kcal/mol
Surface area57640 Å2
MethodPISA
4
A: RAN
B: NUCLEAR PORE COMPLEX PROTEIN NUP358
hetero molecules

C: RAN
D: NUCLEAR PORE COMPLEX PROTEIN NUP358
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8678
Polymers77,7744
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11370 Å2
ΔGint-62 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.339, 139.463, 91.654
Angle α, β, γ (deg.)90.00, 135.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9936, -0.046, 0.1032), (-0.043, -0.9986, -0.0307), (0.1044, 0.0261, -0.9942)
Vector: -4.6952, -12.1015, 63.5246)

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Components

#1: Protein RAN


Mass: 23183.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: GST-FUSION / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62826
#2: Protein NUCLEAR PORE COMPLEX PROTEIN NUP358


Mass: 15703.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: GST-FUSION / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P49792
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.25 / Details: pH 6.25
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG400011
2250 mMammonium sulfate11
3100 mMMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 20286 / % possible obs: 86 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 75.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.1
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.1 / % possible all: 66
Reflection
*PLUS
Num. measured all: 90705
Reflection shell
*PLUS
% possible obs: 66 %

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Processing

Software
NameVersionClassification
CNS0.4refinement
XDSdata reduction
XSCALEdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RAN-GDP

Resolution: 2.96→12.5 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1676 10 %RANDOM
Rwork0.252 ---
obs0.252 17709 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4 Å2 / ksol: 0.24 e/Å3
Displacement parametersBiso mean: 56.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.96→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 64 2 36 5404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3GNP.PAR
X-RAY DIFFRACTION4WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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