[English] 日本語
Yorodumi
- EMDB-17116: CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17116
TitleCAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
Map data
Sample
  • Complex: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2-CyclinE-DCNL1
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Cullin-associated NEDD8-dissociated protein 1
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: S-phase kinase-associated protein 2
    • Protein or peptide: DCN1-like protein 1
  • Ligand: ZINC ION
KeywordsCAND1 / substrate receptor exchange factor / cullin-RING ligase / CRL / SCF / ligase / neddylation / DCNL1 co-E3 / ubiquitin signaling
Function / homology
Function and homology information


positive regulation of protein neddylation / SCF complex assembly / ubiquitin-like protein binding / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of catalytic activity / F-box domain binding / cellular response to cell-matrix adhesion / regulation of protein neddylation / Aberrant regulation of mitotic exit in cancer due to RB1 defects ...positive regulation of protein neddylation / SCF complex assembly / ubiquitin-like protein binding / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of catalytic activity / F-box domain binding / cellular response to cell-matrix adhesion / regulation of protein neddylation / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / Cul4A-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / positive regulation of intracellular estrogen receptor signaling pathway / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / cullin family protein binding / protein K63-linked ubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of protein ubiquitination / protein monoubiquitination / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / positive regulation of double-strand break repair via homologous recombination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / TBP-class protein binding / T cell activation / Vpu mediated degradation of CD4 / Degradation of DVL / molecular function activator activity / Dectin-1 mediated noncanonical NF-kB signaling / animal organ morphogenesis / Activation of NF-kappaB in B cells / Iron uptake and transport / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / DNA Damage Recognition in GG-NER / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / positive regulation of smooth muscle cell proliferation / cellular response to amino acid stimulus / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / negative regulation of canonical Wnt signaling pathway / G1/S transition of mitotic cell cycle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Formation of Incision Complex in GG-NER / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / beta-catenin binding / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER
Similarity search - Function
TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / HEAT-like repeat ...TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / HEAT-like repeat / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / UBA-like superfamily / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / S-phase kinase-associated protein 2 / Cullin-1 / Cullin-associated NEDD8-dissociated protein 1 / DCN1-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsShaaban M / Clapperton JA / Ding S / Maeots ME / Enchev RI / Maslen S / Skehel JM
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
Cancer Research UKCC2059 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2059 United Kingdom
Wellcome TrustCC2059 United Kingdom
CitationJournal: Mol Cell / Year: 2023
Title: Structural and mechanistic insights into the CAND1-mediated SCF substrate receptor exchange.
Authors: Mohammed Shaaban / Julie A Clapperton / Shan Ding / Simone Kunzelmann / Märt-Erik Mäeots / Sarah L Maslen / J Mark Skehel / Radoslav I Enchev /
Abstract: Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment ...Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment and subsequent proteasomal degradation. CAND proteins are essential for the efficient and timely exchange of SRs. To gain structural understanding of the underlying molecular mechanism, we reconstituted a human CAND1-driven exchange reaction of substrate-bound SCF alongside its co-E3 ligase DCNL1 and visualized it by cryo-EM. We describe high-resolution structural intermediates, including a ternary CAND1-SCF complex, as well as conformational and compositional intermediates representing SR- or CAND1-dissociation. We describe in molecular detail how CAND1-induced conformational changes in CUL1/RBX1 provide an optimized DCNL1-binding site and reveal an unexpected dual role for DCNL1 in CAND1-SCF dynamics. Moreover, a partially dissociated CAND1-SCF conformation accommodates cullin neddylation, leading to CAND1 displacement. Our structural findings, together with functional biochemical assays, help formulate a detailed model for CAND-SCF regulation.
History
DepositionApr 13, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17116.png

Downloads & links

-
Map

FileDownload / File: emd_17116.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0265
Minimum - Maximum-0.0016805321 - 1.6426727
Average (Standard dev.)0.0009141417 (±0.021327596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_17116_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17116_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2-CyclinE-DCNL1

EntireName: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2-CyclinE-DCNL1
Components
  • Complex: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2-CyclinE-DCNL1
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Cullin-associated NEDD8-dissociated protein 1
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: S-phase kinase-associated protein 2
    • Protein or peptide: DCN1-like protein 1
  • Ligand: ZINC ION

-
Supramolecule #1: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2-CyclinE-DCNL1

SupramoleculeName: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2-CyclinE-DCNL1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.730672 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG SAGSAAGSGA GWSHPQFEKL EVLFQGPMSS TRSQNPHGLK QIGLDQIWDD LRAGIQQVYT RQSMAKSRYM ELYTHVYNY CTSVHQSNQA RGAGVPPSKS KKGQTPGGAQ FVGLELYKRL KEFLKNYLTN LLKDGEDLMD ESVLKFYTQQ W EDYRFSSK ...String:
MWSHPQFEKG SAGSAAGSGA GWSHPQFEKL EVLFQGPMSS TRSQNPHGLK QIGLDQIWDD LRAGIQQVYT RQSMAKSRYM ELYTHVYNY CTSVHQSNQA RGAGVPPSKS KKGQTPGGAQ FVGLELYKRL KEFLKNYLTN LLKDGEDLMD ESVLKFYTQQ W EDYRFSSK VLNGICAYLN RHWVRRECDE GRKGIYEIYS LALVTWRDCL FRPLNKQVTN AVLKLIEKER NGETINTRLI SG VVQSYVE LGLNEDDAFA KGPTLTVYKE SFESQFLADT ERFYTRESTE FLQQNPVTEY MKKAEARLLE EQRRVQVYLH EST QDELAR KCEQVLIEKH LEIFHTEFQN LLDADKNEDL GRMYNLVSRI QDGLGELKKL LETHIHNQGL AAIEKCGEAA LNDP KMYVQ TVLDVHKKYN ALVMSAFNND AGFVAALDKA CGRFINNNAV TKMAQSSSKS PELLARYCDS LLKKSSKNPE EAELE DTLN QVMVVFKYIE DKDVFQKFYA KMLAKRLVHQ NSASDDAEAS MISKLKQACG FEYTSKLQRM FQDIGVSKDL NEQFKK HLT NSEPLDLDFS IQVLSSGSWP FQQSCTFALP SELERSYQRF TAFYASRHSG RKLTWLYQLS KGELVTNCFK NRYTLQA ST FQMAILLQYN TEDAYTVQQL TDSTQIKMDI LAQVLQILLK SKLLVLEDEN ANVDEVELKP DTLIKLYLGY KNKKLRVN I NVPMKTEQKQ EQETTHKNIE EDRKLLIQAA IVRIMKMRKV LKHQQLLGEV LTQLSSRFKP RVPVIKKCID ILIEKEYLE RVDGEKDTYS YLA

UniProtKB: Cullin-1

-
Macromolecule #2: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

-
Macromolecule #3: Cullin-associated NEDD8-dissociated protein 1

MacromoleculeName: Cullin-associated NEDD8-dissociated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.358219 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSPEFPGRMA SASYHISNLL EKMTSSDKDF RFMATNDLMT ELQKDSIKLD DDSERKVVKM ILKLLEDKNG EVQNLAVKCL GPLVSKVKE YQVETIVDTL CTNMLSDKEQ LRDISSIGLK TVIGELPPAS SGSALAANVC KKITGRLTSA IAKQEDVSVQ L EALDIMAD ...String:
GSPEFPGRMA SASYHISNLL EKMTSSDKDF RFMATNDLMT ELQKDSIKLD DDSERKVVKM ILKLLEDKNG EVQNLAVKCL GPLVSKVKE YQVETIVDTL CTNMLSDKEQ LRDISSIGLK TVIGELPPAS SGSALAANVC KKITGRLTSA IAKQEDVSVQ L EALDIMAD MLSRQGGLLV NFHPSILTCL LPQLTSPRLA VRKRTIIALG HLVMSCGNIV FVDLIEHLLS ELSKNDSMST TR TYIQCIA AISRQAGHRI GEYLEKIIPL VVKFCNVDDD ELREYCIQAF ESFVRRCPKE VYPHVSTIIN ICLKYLTYDP NYN YDDEDE DENAMDADGG DDDDQGSDDE YSDDDDMSWK VRRAAAKCLD AVVSTRHEML PEFYKTVSPA LISRFKEREE NVKA DVFHA YLSLLKQTRP VQSWLCDPDA MEQGETPLTM LQSQVPNIVK ALHKQMKEKS VKTRQCCFNM LTELVNVLPG ALTQH IPVL VPGIIFSLND KSSSSNLKID ALSCLYVILC NHSPQVFHPH VQALVPPVVA CVGDPFYKIT SEALLVTQQL VKVIRP LDQ PSSFDATPYI KDLFTCTIKR LKAADIDQEV KERAISCMGQ IICNLGDNLG SDLPNTLQIF LERLKNEITR LTTVKAL TL IAGSPLKIDL RPVLGEGVPI LASFLRKNQR ALKLGTLSAL DILIKNYSDS LTAAMIDAVL DELPPLISES DMHVSQMA I SFLTTLAKVY PSSLSKISGS ILNELIGLVR SPLLQGGALS AMLDFFQALV VTGTNNLGYM DLLRMLTGPV YSQSTALTH KQSYYSIAKC VAALTRACPK EGPAVVGQFI QDVKNSRSTD SIRLLALLSL GEVGHHIDLS GQLELKSVIL EAFSSPSEEV KSAASYALG SISVGNLPEY LPFVLQEITS QPKRQYLLLH SLKEIISSAS VVGLKPYVEN IWALLLKHCE CAEEGTRNVV A ECLGKLTL IDPETLLPRL KGYLISGSSY ARSSVVTAVK FTISDHPQPI DPLLKNCIGD FLKTLEDPDL NVRRVALVTF NS AAHNKPS LIRDLLDTVL PHLYNETKVR KELIREVEMG PFKHTVDDGL DIRKAAFECM YTLLDSCLDR LDIFEFLNHV EDG LKDHYD IKMLTFLMLV RLSTLCPSAV LQRLDRLVEP LRATCTTKVK ANSVKQEFEK QDELKRSAMR AVAALLTIPE AEKS PLMSE FQSQISSNPE LAAIFESIQK DSSSTNLESM DTS

UniProtKB: Cullin-associated NEDD8-dissociated protein 1

-
Macromolecule #4: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

-
Macromolecule #5: S-phase kinase-associated protein 2

MacromoleculeName: S-phase kinase-associated protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.335312 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSPEFMHRKH LQEIPDLSSN VATSFTWGWD SSKTSELLSG MGVSALEKEE PDSENIPQEL LSNLGHPESP PRKRLKSKGS DKDFVIVRR PKLNRENFPG VSWDSLPDEL LLGIFSCLCL PELLKVSGVC KRWYRLASDE SLWQTLDLTG KNLHPDVTGR L LSQGVIAF ...String:
GSPEFMHRKH LQEIPDLSSN VATSFTWGWD SSKTSELLSG MGVSALEKEE PDSENIPQEL LSNLGHPESP PRKRLKSKGS DKDFVIVRR PKLNRENFPG VSWDSLPDEL LLGIFSCLCL PELLKVSGVC KRWYRLASDE SLWQTLDLTG KNLHPDVTGR L LSQGVIAF RCPRSFMDQP LAEHFSPFRV QHMDLSNSVI EVSTLHGILS QCSKLQNLSL EGLRLSDPIV NTLAKNSNLV RL NLSGCSG FSEFALQTLL SSCSRLDELN LSWCFDFTEK HVQVAVAHVS ETITQLNLSG YRKNLQKSDL STLVRRCPNL VHL DLSDSV MLKNDCFQEF FQLNYLQHLS LSRCYDIIPE TLLELGEIPT LKTLQVFGIV PDGTLQLLKE ALPHLQINCS HFTT IARPT IGNKKNQEIW GIKCRLTLQK PSCL

UniProtKB: S-phase kinase-associated protein 2

-
Macromolecule #6: DCN1-like protein 1

MacromoleculeName: DCN1-like protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.304439 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMNKLKSSQ KDKVRQFMIF TQSSEKTAVS CLSQNDWKLD VATDNFFQNP ELYIRESVKG SLDRKKLEQL YNRYKDPQDE NKIGIDGIQ QFCDDLALDP ASISVLIIAW KFRAATQCEF SKQEFMDGMT ELGCDSIEKL KAQIPKMEQE LKEPGRFKDF Y QFTFNFAK ...String:
GSMNKLKSSQ KDKVRQFMIF TQSSEKTAVS CLSQNDWKLD VATDNFFQNP ELYIRESVKG SLDRKKLEQL YNRYKDPQDE NKIGIDGIQ QFCDDLALDP ASISVLIIAW KFRAATQCEF SKQEFMDGMT ELGCDSIEKL KAQIPKMEQE LKEPGRFKDF Y QFTFNFAK NPGQKGLDLE MAIAYWNLVL NGRFKFLDLW NKFLLEHHKR SIPKDTWNLL LDFSTMIADD MSNYDEEGAW PV LIDDFVE FARPQIAGTK STTV

UniProtKB: DCN1-like protein 1

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
25.0 mMHEPES
150.0 mMNaCl
1.0 mMTCEP
0.1 percentoctyl glucoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1u6g

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 735959
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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