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- EMDB-44631: Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron -

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Basic information

Entry
Database: EMDB / ID: EMD-44631
TitleHuman CRL-2 ZYG11B binding to human NLRP1 Gly/N degron
Map data
Sample
  • Complex: human CRL2-ZYG11B E3 ligase complex
    • Protein or peptide: Protein zyg-11 homolog B
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-2
    • Protein or peptide: Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
  • Ligand: ZINC ION
KeywordsGly/N degron / Cullin E3 ligase / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


NLRP1 inflammasome complex / self proteolysis / NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity involved in apoptotic process / The NLRP1 inflammasome / NLRP3 inflammasome complex / cysteine-type endopeptidase activator activity / negative regulation of beige fat cell differentiation / response to muramyl dipeptide / cullin-RING-type E3 NEDD8 transferase ...NLRP1 inflammasome complex / self proteolysis / NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity involved in apoptotic process / The NLRP1 inflammasome / NLRP3 inflammasome complex / cysteine-type endopeptidase activator activity / negative regulation of beige fat cell differentiation / response to muramyl dipeptide / cullin-RING-type E3 NEDD8 transferase / canonical inflammasome complex / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / target-directed miRNA degradation / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / elongin complex / Cul7-RING ubiquitin ligase complex / VCB complex / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation of protein autoubiquitination / protein neddylation / regulation of BMP signaling pathway / NEDD8 ligase activity / regulation of mitophagy / Hydrolases; Acting on peptide bonds (peptidases) / cellular response to UV-B / negative regulation of response to oxidative stress / regulation of centrosome duplication / protein K27-linked ubiquitination / positive regulation of cilium assembly / Cul5-RING ubiquitin ligase complex / pattern recognition receptor signaling pathway / ubiquitin-ubiquitin ligase activity / regulation of TOR signaling / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / SCF ubiquitin ligase complex / regulation of DNA damage checkpoint / regulation of mitotic cytokinesis / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / pattern recognition receptor activity / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / nucleotide-excision repair complex / regulation of cell cycle phase transition / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / protein quality control for misfolded or incompletely synthesized proteins / Cul4B-RING E3 ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / regulation of cellular response to stress / limb development / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / pyroptotic inflammatory response / protein monoubiquitination / cullin family protein binding / neuron apoptotic process / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / centrosome duplication / regulation of DNA-templated DNA replication initiation / Formation of HIV elongation complex in the absence of HIV Tat / cilium assembly / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / protein K63-linked ubiquitination / RNA Polymerase II Pre-transcription Events / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / protein K48-linked ubiquitination / activation of innate immune response / signaling adaptor activity / transcription-coupled nucleotide-excision repair / post-translational protein modification / positive regulation of TORC1 signaling / regulation of embryonic development / replication fork processing / cellular response to amino acid stimulus / transcription corepressor binding / regulation of mitotic cell cycle / negative regulation of canonical NF-kappaB signal transduction / positive regulation of interleukin-1 beta production
Similarity search - Function
: / : / Protein zer-1 homolog-like, C-terminal domain / Zer-1-like, Leucine-rich repeats / : / FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain ...: / : / Protein zer-1 homolog-like, C-terminal domain / Zer-1-like, Leucine-rich repeats / : / FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain profile. / NACHT domain / NACHT nucleoside triphosphatase / NACHT-NTPase domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / CARD domain / CARD caspase recruitment domain profile. / Elongin-C / : / Elongin B / Caspase recruitment domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Leucine Rich repeat / Cullin alpha solenoid domain / Cullin / Leucine Rich Repeat / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Death-like domain superfamily / Leucine-rich repeat profile. / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Armadillo-type fold / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-2 / Elongin-C / Elongin-B / NACHT, LRR and PYD domains-containing protein 1 / Protein zyg-11 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLiu X / Gross JD
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 25, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44631.png

Downloads & links

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Map

FileDownload / File: emd_44631.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 360 pix.
= 300.6 Å		0.84 Å/pix.
x 360 pix.
= 300.6 Å		0.84 Å/pix.
x 360 pix.
= 300.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-20.927541999999999 - 39.927753000000003
Average (Standard dev.)0.000000000007046 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44631_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44631_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : human CRL2-ZYG11B E3 ligase complex

EntireName: human CRL2-ZYG11B E3 ligase complex
Components
  • Complex: human CRL2-ZYG11B E3 ligase complex
    • Protein or peptide: Protein zyg-11 homolog B
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-2
    • Protein or peptide: Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
  • Ligand: ZINC ION

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Supramolecule #1: human CRL2-ZYG11B E3 ligase complex

SupramoleculeName: human CRL2-ZYG11B E3 ligase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 230 kDa/nm

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Macromolecule #1: Protein zyg-11 homolog B

MacromoleculeName: Protein zyg-11 homolog B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.463344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SHMVDPEDQA GAAMEEASPY SLLDICLNFL TTHLEKFCSA RQDGTLCLQE PGVFPQEVAD RLLRTMAFHG LLNDGTVGIF RGNQMRLKR ACIRKAKISA VAFRKAFCHH KLVELDATGV NADITITDII SGLGSNKWIQ QNLQCLVLNS LTLSLEDPYE R CFSRLSGL ...String:
SHMVDPEDQA GAAMEEASPY SLLDICLNFL TTHLEKFCSA RQDGTLCLQE PGVFPQEVAD RLLRTMAFHG LLNDGTVGIF RGNQMRLKR ACIRKAKISA VAFRKAFCHH KLVELDATGV NADITITDII SGLGSNKWIQ QNLQCLVLNS LTLSLEDPYE R CFSRLSGL RALSITNVLF YNEDLAEVAS LPRLESLDIS NTSITDITAL LACKDRLKSL TMHHLKCLKM TTTQILDVVR EL KHLNHLD ISDDKQFTSD IALRLLEQKD ILPNLVSLDV SGRKHVTDKA VEAFIQQRPS MQFVGLLATD AGYSEFLTGE GHL KVSGEA NETQIAEALK RYSERAFFVR EALFHLFSLT HVMEKTKPEI LKLVVTGMRN HPMNLPVQLA ASACVFNLTK QDLA AGMPV RLLADVTHLL LKAMEHFPNH QQLQKNCLLS LCSDRILQDV PFNRFEAAKL VMQWLCNHED QNMQRMAVAI ISILA AKLS TEQTAQLGTE LFIVRQLLQI VKQKTNQNSV DTTLKFTLSA LWNLTDESPT TCRHFIENQG LELFMRVLES FPTESS IQQ KVLGLLNNIA EVQELHSELM WKDFIDHISS LLHSVEVEVS YFAAGIIAHL ISRGEQAWTL SRSQRNSLLD DLHSAIL KW PTPECEMVAY RSFNPFFPLL GCFTTPGVQL WAVWAMQHVC SKNPSRYCSM LIEEGGLQHL YNIKDHEHTD PHVQQIAV A ILDSLEKHIV RHGRPPPCKK QPQARLN

UniProtKB: Protein zyg-11 homolog B

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Macromolecule #2: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

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Macromolecule #4: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.428453 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK ...String:
MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK NDRGGEDPNQ KVIHGVINSF VHVEQYKKKF PLKFYQEIFE SPFLTETGEY YKQEASNLLQ ESNCSQYMEK VL GRLKDEE IRCRKYLHPS SYTKVIHECQ QRMVADHLQF LHAECHNIIR QEKKNDMANM YVLLRAVSTG LPHMIQELQN HIH DEGLRA TSNLTQENMP TLFVESVLEV HGKFVQLINT VLNGDQHFMS ALDKALTSVV NYREPKSVCK APELLAKYCD NLLK KSAKG MTENEVEDRL TSFITVFKYI DDKDVFQKFY ARMLAKRLIH GLSMSMDSEE AMINKLKQAC GYEFTSKLHR MYTDM SVSA DLNNKFNNFI KNQDTVIDLG ISFQIYVLQA GAWPLTQAPS STFAIPQELE KSVQMFELFY SQHFSGRKLT WLHYLC TGE VKMNYLGKPY VAMVTTYQMA VLLAFNNSET VSYKELQDST QMNEKELTKT IKSLLDVKMI NHDSEKEDID AESSFSL NM NFSSKRTKFK ITTSMQKDTP QEMEQTRSAV DEDRKMYLQA AIVRIMKARK VLRHNALIQE VISQSRARFN PSISMIKK C IEVLIDKQYI ERSQASADEY SYVALEGGGG WSHPQFEKGG GSGGGSGGGS WSHPQFEK

UniProtKB: Cullin-2

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Macromolecule #5: Peptide from NACHT, LRR and PYD domains-containing protein 1, N-t...

MacromoleculeName: Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.124516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSERRVLRQ(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

UniProtKB: NACHT, LRR and PYD domains-containing protein 1

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Macromolecule #6: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #7: ZINC ION

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

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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

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 20.0 µm / Nominal defocus min: 5.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: ALGEBRAIC (ARTS) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80380
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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