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- EMDB-44238: Overall map for the RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain from ... -

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Entry
Database: EMDB / ID: EMD-44238
TitleOverall map for the RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain from human RANBP2/RAN(GTP)/SUMO1-RANGAP1/UBC9/CRM1/RAN(GTP) complex
Map dataOverall map for RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain from human RANBP2/RAN(GTP)/SUMO1-RANGAP1/UBC9/CRM1/RAN(GTP) complex
Sample
  • Complex: Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex
    • Protein or peptide: Exportin-1
    • Protein or peptide: GTP-binding nuclear protein Ran(Q69L)
    • Protein or peptide: SUMO-conjugating enzyme UBC9
    • Protein or peptide: Small ubiquitin-related modifier 1 (Q94P)
    • Protein or peptide: Nucleoporin - E3 SUMO-protein ligase RanBP2
    • Protein or peptide: Ran GTPase-activating protein 1
Keywordskaryopherin / SUMO E3 / SUMO E2 / transporter / GTPase / GTPase activating protein / exportin / G-protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


: / cellular response to vasopressin / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / HuR (ELAVL1) binds and stabilizes mRNA / SUMO ligase complex / protein localization to nuclear pore / SUMO ligase activity / negative regulation of transcription by transcription factor localization ...: / cellular response to vasopressin / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / HuR (ELAVL1) binds and stabilizes mRNA / SUMO ligase complex / protein localization to nuclear pore / SUMO ligase activity / negative regulation of transcription by transcription factor localization / transferase complex / annulate lamellae / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / Vitamin D (calciferol) metabolism / pre-miRNA export from nucleus / RNA nuclear export complex / nuclear pore cytoplasmic filaments / mitotic nuclear membrane reassembly / snRNA import into nucleus / synaptonemal complex / regulation of centrosome duplication / nuclear export signal receptor activity / Nuclear Pore Complex (NPC) Disassembly / small protein activating enzyme binding / negative regulation of action potential / 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) / SUMOylation of DNA methylation proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / regulation of protein export from nucleus / Transport of Mature mRNA Derived from an Intronless Transcript / activation of GTPase activity / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Maturation of nucleoprotein / negative regulation of protein export from nucleus / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / nuclear export / regulation of cardiac muscle cell contraction / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / GTP metabolic process / Transferases; Acyltransferases; Aminoacyltransferases / tRNA processing in the nucleus / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / nucleocytoplasmic transport / aggresome / Maturation of nucleoprotein / centrosome localization / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / regulation of gluconeogenesis / DNA metabolic process / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / transcription factor binding / ubiquitin-specific protease binding / Vpr-mediated nuclear import of PICs / Maturation of hRSV A proteins / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / mitotic sister chromatid segregation / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / mRNA transport / response to axon injury / viral process / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore
Similarity search - Function
Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Small ubiquitin-related modifier 1, Ubl domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 ...Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Small ubiquitin-related modifier 1, Ubl domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / 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 / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Leucine rich repeat, ribonuclease inhibitor type / : / Zinc finger domain / Leucine Rich repeat / 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 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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 / Ubiquitin-conjugating enzyme/RWD-like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich 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 / Leucine-rich repeat domain superfamily / Armadillo-like helical / Small GTP-binding protein domain / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / PH-like domain superfamily / Armadillo-type fold / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exportin-1 / Ran GTPase-activating protein 1 / E3 SUMO-protein ligase RanBP2 / GTP-binding nuclear protein Ran / Small ubiquitin-related modifier 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsLima CD / DiMattia MA
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
CitationJournal: bioRxiv / Year: 2024
Title: Structural basis for a nucleoporin exportin complex between RanBP2, SUMO1-RanGAP1, the E2 Ubc9, Crm1 and the Ran GTPase.
Authors: Vladimir Baytshtok / Michael A DiMattia / Christopher D Lima /
Abstract: The human nucleoporin RanBP2/Nup358 interacts with SUMO1-modified RanGAP1 and the SUMO E2 Ubc9 at the nuclear pore complex (NPC) to promote export and disassembly of exportin Crm1/Ran(GTP)/cargo ...The human nucleoporin RanBP2/Nup358 interacts with SUMO1-modified RanGAP1 and the SUMO E2 Ubc9 at the nuclear pore complex (NPC) to promote export and disassembly of exportin Crm1/Ran(GTP)/cargo complexes. In mitosis, RanBP2/SUMO1-RanGAP1/Ubc9 remains intact after NPC disassembly and is recruited to kinetochores and mitotic spindles by Crm1 where it contributes to mitotic progression. Interestingly, RanBP2 binds SUMO1-RanGAP1/Ubc9 via motifs that also catalyze SUMO E3 ligase activity. Here, we resolve cryo-EM structures of a RanBP2 C-terminal fragment in complex with Crm1, SUMO1-RanGAP1/Ubc9, and two molecules of Ran(GTP). These structures reveal several unanticipated interactions with Crm1 including a nuclear export signal (NES) for RanGAP1, the deletion of which mislocalizes RanGAP1 and the Ran GTPase in cells. Our structural and biochemical results support models in which RanBP2 E3 ligase activity is dependent on Crm1, the RanGAP1 NES and Ran GTPase cycling.
History
DepositionMar 23, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44238.png

Downloads & links

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Map

FileDownload / File: emd_44238.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map for RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain from human RANBP2/RAN(GTP)/SUMO1-RANGAP1/UBC9/CRM1/RAN(GTP) complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 220 pix.
= 239.36 Å		1.09 Å/pix.
x 220 pix.
= 239.36 Å		1.09 Å/pix.
x 220 pix.
= 239.36 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.20296507 - 0.35364193
Average (Standard dev.)0.00023863146 (±0.0056694667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 239.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 for RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain...

Fileemd_44238_half_map_1.map
AnnotationHalf map 1 for RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain from human RANBP2/RAN(GTP)/SUMO1-RANGAP1/UBC9/CRM1/RAN(GTP) complex
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain...

Fileemd_44238_half_map_2.map
AnnotationHalf map 2 for RANBP2 RBD4/RAN(GTP)/RANGAP1 GAP domain from human RANBP2/RAN(GTP)/SUMO1-RANGAP1/UBC9/CRM1/RAN(GTP) complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex

EntireName: Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex
Components
  • Complex: Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex
    • Protein or peptide: Exportin-1
    • Protein or peptide: GTP-binding nuclear protein Ran(Q69L)
    • Protein or peptide: SUMO-conjugating enzyme UBC9
    • Protein or peptide: Small ubiquitin-related modifier 1 (Q94P)
    • Protein or peptide: Nucleoporin - E3 SUMO-protein ligase RanBP2
    • Protein or peptide: Ran GTPase-activating protein 1

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Supramolecule #1: Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex

SupramoleculeName: Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: SUMO1 Gly97 is covalently linked to RANGAP1 Lys524 through a isopeptide bond
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Exportin-1

MacromoleculeName: Exportin-1 / type: protein_or_peptide / ID: 1
Details: SHM N-terminal amino acids remnants of expression tag
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SHMMPAIMTM LADHAARQLL DFSQKLDINL LDNVVNCLYH GEGAQQRMAQ EVLTHLKEHP DAWTRVDTIL EFSQNMNTKY YGLQILENV IKTRWKILPR NQCEGIKKYV VGLIIKTSSD PTCVEKEKVY IGKLNMILVQ ILKQEWPKHW PTFISDIVGA S RTSESLCQ ...String:
SHMMPAIMTM LADHAARQLL DFSQKLDINL LDNVVNCLYH GEGAQQRMAQ EVLTHLKEHP DAWTRVDTIL EFSQNMNTKY YGLQILENV IKTRWKILPR NQCEGIKKYV VGLIIKTSSD PTCVEKEKVY IGKLNMILVQ ILKQEWPKHW PTFISDIVGA S RTSESLCQ NNMVILKLLS EEVFDFSSGQ ITQVKSKHLK DSMCNEFSQI FQLCQFVMEN SQNAPLVHAT LETLLRFLNW IP LGYIFET KLISTLIYKF LNVPMFRNVS LKCLTEIAGV SVSQYEEQFV TLFTLTMMQL KQMLPLNTNI RLAYSNGKDD EQN FIQNLS LFLCTFLKEH DQLIEKRLNL RETLMEALHY MLLVSEVEET EIFKICLEYW NHLAAELYRE SPFSTSASPL LSGS QHFDV PPRRQLYLPM LFKVRLLMVS RMAKPEEVLV VENDQGEVVR EFMKDTDSIN LYKNMRETLV YLTHLDYVDT ERIMT EKLH NQVNGTEWSW KNLNTLCWAI GSISGAMHEE DEKRFLVTVI KDLLGLCEQK RGKDNKAIIA SNIMYIVGQY PRFLRA HWK FLKTVVNKLF EFMHETHDGV QDMACDTFIK IAQKCRRHFV QVQVGEVMPF IDEILNNINT IICDLQPQQV HTFYEAV GY MIGAQTDQTV QEHLIEKYML LPNQVWDSII QQATKNVDIL KDPETVKQLG SILKTNVRAC KAVGHPFVIQ LGRIYLDM L NVYKCLSENI SAAIQANGEM VTKQPLIRSM RTVKRETLKL ISGWVSRSND PQMVAENFVP PLLDAVLIDY QRNVPAARE PEVLSTMAII VNKLGGHITA EIPQIFDAVF ECTLNMINKD FEEYPEHRTN FFLLLQAVNS HCFPAFLAIP PTQFKLVLDS IIWAFKHTM RNVADTGLQI LFTLLQNVAQ EEAAAQSFYQ TYFCDILQHI FSVVTDTSHT AGLTMHASIL AYMFNLVEEG K ISTSLNPG NPVNNQIFLQ EYVANLLKSA FPHLQDAQVK LFVTGLFSLN QDIPAFKEHL RDFLVQIKEF AGEDTSDLFL EE REIALRQ ADEEKHKRQM SVPGIFNPHE IPEEMCD

UniProtKB: Exportin-1

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Macromolecule #2: GTP-binding nuclear protein Ran(Q69L)

MacromoleculeName: GTP-binding nuclear protein Ran(Q69L) / type: protein_or_peptide / ID: 2
Details: GSHMAS N-terminal amino acids residual after removal of purification epitope tag
Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMASMAAQ GEPQVQFKLV LVGDGGTGKT TFVKRHLTGE FEKKYVATLG VEVHPLVFHT NRGPIKFNVW DTAGLEKFGG LRDGYYIQA QCAIIMFDVT SRVTYKNVPN WHRDLVRVCE NIPIVLCGNK VDIKDRKVKA KSIVFHRKKN LQYYDISAKS N YNFEKPFL ...String:
GSHMASMAAQ GEPQVQFKLV LVGDGGTGKT TFVKRHLTGE FEKKYVATLG VEVHPLVFHT NRGPIKFNVW DTAGLEKFGG LRDGYYIQA QCAIIMFDVT SRVTYKNVPN WHRDLVRVCE NIPIVLCGNK VDIKDRKVKA KSIVFHRKKN LQYYDISAKS N YNFEKPFL WLARKLIGDP NLEFVAMPAL APPEVVMDPA LAAQYEHDLE VAQTTALPDE DDDL

UniProtKB: GTP-binding nuclear protein Ran

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Macromolecule #3: SUMO-conjugating enzyme UBC9

MacromoleculeName: SUMO-conjugating enzyme UBC9 / type: protein_or_peptide / ID: 3
Details: GSH N-terminal amino acids left over after cleavage of affinity tag
Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGIALS RLAQERKAWR KDHPFGFVAV PTKNPDGTMN LMNWECAIPG KKGTPWEGGL FKLRMLFKDD YPSSPPKCKF EPPLFHPNV YPSGTVCLSI LEEDKDWRPA ITIKQILLGI QELLNEPNIQ DPAQAEAYTI YCQNRVEYEK RVRAQAKKFA P S

UniProtKB: SUMO-conjugating enzyme UBC9

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Macromolecule #4: Small ubiquitin-related modifier 1 (Q94P)

MacromoleculeName: Small ubiquitin-related modifier 1 (Q94P) / type: protein_or_peptide / ID: 4
Details: GSHM N-terminal amino acids left over after cleavage of affinity tag
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMMSDQEA KPSTEDLGDK KEGEYIKLKV IGQDSSEIHF KVKMTTHLKK LKESYCQRQG VPMNSLRFLF EGQRIADNHT PKELGMEEE DVIEVYQEPT GG

UniProtKB: Small ubiquitin-related modifier 1

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Macromolecule #5: Nucleoporin - E3 SUMO-protein ligase RanBP2

MacromoleculeName: Nucleoporin - E3 SUMO-protein ligase RanBP2 / type: protein_or_peptide / ID: 5
Details: GSH N-terminal amino acids left after cleavage of affinity tag
Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMDSLITP HVSRSSTPRE SPCGKIAVAV LEETTRERTD VIQGDDVADA TSEVEVSSTS ETTPKAVVSP PKFVFGSESV KSIFSSEKS KPFAFGNSSA TGSLFGFSFN APLKSNNSET SSVAQSGSES KVEPKKCELS KNSDIEQSSD SKVKNLFASF P TEESSINY ...String:
GSHMDSLITP HVSRSSTPRE SPCGKIAVAV LEETTRERTD VIQGDDVADA TSEVEVSSTS ETTPKAVVSP PKFVFGSESV KSIFSSEKS KPFAFGNSSA TGSLFGFSFN APLKSNNSET SSVAQSGSES KVEPKKCELS KNSDIEQSSD SKVKNLFASF P TEESSINY TFKTPEKAKE KKKPEDSPSD DDVLIVYELT PTAEQKALAT KLKLPPTFFC YKNRPDYVSE EEEDDEDFET AV KKLNGKL YLDGSEKCRP LEENTADNEK ECIIVWEKKP TVEEKAKADT LKLPPTFFCG VCSDTDEDNG NGEDFQSELQ KVQ EAQKSQ TEEITSTTDS VYTGGTEVMV PSFCKSEEPD SITKSISSPS VSSETMDKPV DLSTRKEIDT DSTSQGESKI VSFG FGSST GLSFADLASS NSGDFAFGSK DKNFQWANTG AAVFGTQSVG TQSAGKVGED EDGSDEEVVH NEDIHFEPIV SLPEV EVKS GEEDEEILFK ERAKLYRWDR DVSQWKERGV GDIKILWHTM KNYYRILMRR DQVFKVCANH VITKTMELKP LNVSNN ALV WTASDYADGE AKVEQLAVRF KTKEVADCFK KTFEECQQNL MKLQKGHVSL AAELSK

UniProtKB: E3 SUMO-protein ligase RanBP2

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Macromolecule #6: Ran GTPase-activating protein 1

MacromoleculeName: Ran GTPase-activating protein 1 / type: protein_or_peptide / ID: 6
Details: GSHM N-terminal amino acids left after cleavage of affinity tag
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMMASEDI AKLAETLAKT QVAGGQLSFK GKSLKLNTAE DAKDVIKEIE DFDSLEALRL EGNTVGVEAA RVIAKALEKK SELKRCHWS DMFTGRLRTE IPPALISLGE GLITAGAQLV ELDLSDNAFG PDGVQGFEAL LKSSACFTLQ ELKLNNCGMG I GGGKILAA ...String:
GSHMMASEDI AKLAETLAKT QVAGGQLSFK GKSLKLNTAE DAKDVIKEIE DFDSLEALRL EGNTVGVEAA RVIAKALEKK SELKRCHWS DMFTGRLRTE IPPALISLGE GLITAGAQLV ELDLSDNAFG PDGVQGFEAL LKSSACFTLQ ELKLNNCGMG I GGGKILAA ALTECHRKSS AQGKPLALKV FVAGRNRLEN DGATALAEAF RVIGTLEEVH MPQNGINHPG ITALAQAFAV NP LLRVINL NDNTFTEKGA VAMAETLKTL RQVEVINFGD CLVRSKGAVA IADAIRGGLP KLKELNLSFC EIKRDAALAV AEA MADKAE LEKLDLNGNT LGEEGCEQLQ EVLEGFNMAK VLASLSDDED EEEEEEGEEE EEEAEEEEEE DEEEEEEEEE EEEE EPQQR GQGEKSATPS RKILDPNTGE PAPVLSSPPP ADVSTFLAFP SPEKLLRLGP KSSVLIAQQT DTSDPEKVVS AFLKV SSVF KDEATVRMAV QDAVDALMQK AFNSSSFNSN TFLTRLLVHM GLLKSEDKVK AIANLYGPLM ALNHMVQQDY FPKALA PLL LAFVTKPNSA LESCSFARHS LLQTLYKV

UniProtKB: Ran GTPase-activating protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 8
Details: 20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 30 s wait time, blot for 2.5 s before plunging.
DetailsGel filtered - sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 85.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 895509
Details: This is an overall map resulting from alignments and particle subtraction so particles per map component differ - after selection of particles containing Crm1/Ran(GTP) there were 534708 ...Details: This is an overall map resulting from alignments and particle subtraction so particles per map component differ - after selection of particles containing Crm1/Ran(GTP) there were 534708 unique particles - after selection of particles where RBD4/RAN(GTP)/RANGAP1 GAP could be aligned there were 287278 particles
Startup modelType of model: OTHER / Details: Ab initio model from cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 287278
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3uin

source_name: PDB, initial_model_type: experimental model

3gjx

source_name: PDB, initial_model_type: experimental model

4l6e

source_name: PDB, initial_model_type: experimental model

1k5d

source_name: PDB, initial_model_type: experimental model

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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

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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

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