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- EMDB-15603: Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament -

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Basic information

Entry
Database: EMDB / ID: EMD-15603
TitleCryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament
Map data
Sample
  • Complex: Complex of hCtBP1 with hRAI2
    • Protein or peptide: C-terminal-binding protein 1
    • Protein or peptide: Retinoic acid-induced protein 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
KeywordsComplex / Tumor suppressor / oncogenic / filament assembly / ANTITUMOR PROTEIN
Function / homology
Function and homology information


Signaling by TCF7L2 mutants / Repression of WNT target genes / animal organ development / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / embryo development ending in birth or egg hatching / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / synaptic vesicle endocytosis / white fat cell differentiation ...Signaling by TCF7L2 mutants / Repression of WNT target genes / animal organ development / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / embryo development ending in birth or egg hatching / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / viral genome replication / transcription corepressor binding / SUMOylation of transcription cofactors / Deactivation of the beta-catenin transactivating complex / transcription coregulator binding / transcription corepressor activity / NAD binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Retinoic acid-induced protein 2/sine oculis-binding protein homologue / Sine oculis-binding protein / C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain ...Retinoic acid-induced protein 2/sine oculis-binding protein homologue / Sine oculis-binding protein / C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
C-terminal-binding protein 1 / Retinoic acid-induced protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGoradia N / Mullapudi E / Wilmanns M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)218826742 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament
Authors: Goradia N / Mullapudi E / Wilmanns M
History
DepositionAug 16, 2022-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15603.png

Downloads & links

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Map

FileDownload / File: emd_15603.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 520 pix.
= 452.4 Å		0.87 Å/pix.
x 520 pix.
= 452.4 Å		0.87 Å/pix.
x 520 pix.
= 452.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.37503293 - 1.2275692
Average (Standard dev.)-0.000019628655 (±0.034995906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 452.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15603_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_15603_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of hCtBP1 with hRAI2

EntireName: Complex of hCtBP1 with hRAI2
Components
  • Complex: Complex of hCtBP1 with hRAI2
    • Protein or peptide: C-terminal-binding protein 1
    • Protein or peptide: Retinoic acid-induced protein 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: Complex of hCtBP1 with hRAI2

SupramoleculeName: Complex of hCtBP1 with hRAI2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.0 MDa

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Macromolecule #1: C-terminal-binding protein 1

MacromoleculeName: C-terminal-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.525348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSAGL EVLFQGPMGS SHLLNKGLPL GVRPPIMNGP LHPRPLVALL DGRDCTVEMP ILKDVATVAF CDAQSTQEIH EKVLNEAVG ALMYHTITLT REDLEKFKAL RIIVRIGSGF DNIDIKSAGD LGIAVCNVPA ASVEETADST LCHILNLYRR A TWLHQALR ...String:
HHHHHHSAGL EVLFQGPMGS SHLLNKGLPL GVRPPIMNGP LHPRPLVALL DGRDCTVEMP ILKDVATVAF CDAQSTQEIH EKVLNEAVG ALMYHTITLT REDLEKFKAL RIIVRIGSGF DNIDIKSAGD LGIAVCNVPA ASVEETADST LCHILNLYRR A TWLHQALR EGTRVQSVEQ IREVASGAAR IRGETLGIIG LGRVGQAVAL RAKAFGFNVL FYDPYLSDGV ERALGLQRVS TL QDLLFHS DCVTLHCGLN EHNHHLINDF TVKQMRQGAF LVNTARGGLV DEKALAQALK EGRIRGAALD VHESEPFSFS QGP LKDAPN LICTPHAAWY SEQASIEMRE EAAREIRRAI TGRIPDSLKN CVNKDHLTAA THWASMDPAV VHPELNGAAY RYPP GVVGV APTGIPAAVE GIVPSAMSLS HGLPPVAHPP HAPSPGQTVK PEADRDHASD QL

UniProtKB: C-terminal-binding protein 1

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Macromolecule #2: Retinoic acid-induced protein 2

MacromoleculeName: Retinoic acid-induced protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.252756 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHPMKQ YKLILNGKTL KGETTTEAVD AATAEKVFKQ YANDNGVDGE WTYDDATKTF TVTEGSGSGS ENLYFQGAMD SRHTVIKMG SENEALDLSM KSVPWLKAGA LDLSVAAHRK SEPPPETLYD

UniProtKB: Retinoic acid-induced protein 2

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Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 24 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 189823
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6cdf

Output model

PDB-8ari:
Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament

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