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- EMDB-71964: Hamster Scap/Insig-2 complex with cholesterol and bound Fab4G10 -

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Basic information

Entry
Database: EMDB / ID: EMD-71964
TitleHamster Scap/Insig-2 complex with cholesterol and bound Fab4G10
Map dataMain map
Sample
  • Complex: Scap/Insig-2 complex with bound Fab4G10
    • Complex: Scap/Insig-2 complex
      • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
      • Protein or peptide: Insulin-induced gene protein
    • Complex: Fab4G10
      • Protein or peptide: Fab4G10 heavy chain
      • Protein or peptide: Fab4G10 light chain
  • Ligand: CHOLESTEROL
KeywordsComplex / sterol-binding / COPII-binding / MEMBRANE PROTEIN
Function / homology
Function and homology information


SREBP-SCAP complex retention in endoplasmic reticulum / vesicle coat / SREBP-SCAP-Insig complex / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / sterol binding / SREBP signaling pathway / COPII-coated vesicle cargo loading / cellular response to sterol / cholesterol biosynthetic process ...SREBP-SCAP complex retention in endoplasmic reticulum / vesicle coat / SREBP-SCAP-Insig complex / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / sterol binding / SREBP signaling pathway / COPII-coated vesicle cargo loading / cellular response to sterol / cholesterol biosynthetic process / cholesterol metabolic process / ER to Golgi transport vesicle membrane / cellular response to insulin stimulus / protein import into nucleus / Golgi membrane / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Insulin-induced protein family / Insulin-induced protein (INSIG) / : / : / SCAP N-terminal / SCAP Beta-propeller / Sterol regulatory element-binding protein cleavage-activating protein / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. ...Insulin-induced protein family / Insulin-induced protein (INSIG) / : / : / SCAP N-terminal / SCAP Beta-propeller / Sterol regulatory element-binding protein cleavage-activating protein / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Sterol regulatory element-binding protein cleavage-activating protein / Insulin-induced gene protein
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWilliams BC / Kober DL / Bai X / Radhakrishnan A / Rosenbaum DM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM116387 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL160487 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI158357 United States
CitationJournal: To Be Published
Title: Hamster Scap/Insig-2 bound to cholesterol
Authors: Williams BC / Rosenbaum DM
History
DepositionAug 5, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71964.png

Downloads & links

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Map

FileDownload / File: emd_71964.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055589
Minimum - Maximum-0.021149887 - 0.053191178
Average (Standard dev.)-0.000036097772 (±0.0011189609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer map for model building and illustrations

Fileemd_71964_additional_1.map
AnnotationDeepEMhancer map for model building and illustrations
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_71964_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_71964_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Scap/Insig-2 complex with bound Fab4G10

EntireName: Scap/Insig-2 complex with bound Fab4G10
Components
  • Complex: Scap/Insig-2 complex with bound Fab4G10
    • Complex: Scap/Insig-2 complex
      • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
      • Protein or peptide: Insulin-induced gene protein
    • Complex: Fab4G10
      • Protein or peptide: Fab4G10 heavy chain
      • Protein or peptide: Fab4G10 light chain
  • Ligand: CHOLESTEROL

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Supramolecule #1: Scap/Insig-2 complex with bound Fab4G10

SupramoleculeName: Scap/Insig-2 complex with bound Fab4G10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Supramolecule #2: Scap/Insig-2 complex

SupramoleculeName: Scap/Insig-2 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Supramolecule #3: Fab4G10

SupramoleculeName: Fab4G10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Sterol regulatory element-binding protein cleavage-activating protein

MacromoleculeName: Sterol regulatory element-binding protein cleavage-activating protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Molecular weightTheoretical: 89.014695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKE NLYFQGTGHH HHHHHHTLTE RLREKISQAF YNHGLLCASY PIPIILFTGL CILACCYPL LKLPLPGTGP VEFSTPVKDY SPPPVDSDHK QGEPSEQPEW YVGAPVAYIQ QIFVKSSVSP WHKNLLAVDV F RLPLSRAF ...String:
MDYKDDDDKG SDYKDDDDKG SDYKDDDDKE NLYFQGTGHH HHHHHHTLTE RLREKISQAF YNHGLLCASY PIPIILFTGL CILACCYPL LKLPLPGTGP VEFSTPVKDY SPPPVDSDHK QGEPSEQPEW YVGAPVAYIQ QIFVKSSVSP WHKNLLAVDV F RLPLSRAF QLVEEIRNHA LRDSSGVKSL EEVCLQVTDL LPGLRKLRNL LPEHGCLLLS PGNFWQNDWE RFHADPDIIG TI HQHEPKT LQTSATLKDL LFGVPGKYSG VSLYTRKRTV SYTITLVFQR YDSRFLSSLR SRLKLLHPSP NCSLRAENLV HVH FKEEIG IAELIPLVTT YIILFAYIYF STRKIDMVKS KWGLALAAVV TVLSSLLMSV GLCTLFGLTP TLNGGEIFPY LVVV IGLEN VLVLTKSVVS TPVDLEVKLR IAQGLSSESW SIMKNVATEL GIILIGYFTL VPAIQEFCLF AVVGLVSDFF LQMFF FTTV LSIDIRRMEL ADLNKRLPPE SCLPSAKPVG RPARYERQLA VRPAMPHTIT LQPSSFRNLR LPKRLRVIYF LARTRL AQR LIMAGTVVWI GILVYTDPAG LRTYLAAQVT EQSPLGEGSL GPMPVPSGVL PASRPDPAFS IFPPDAPKLP ENQTVPG EL PEHAAPAEGV HDSRAPEVTW GPEDEELWRR LSFRHWPTLF NYYNITLAKR YISLLPVIPV TLRLNPQEAL EGRQPQDG R SAWAPPESLP AGLWEAGPKG PGGTQAHGDI TLYKVAALGL AAGIVLVLLL LCLYRVLCPR NYGQPGGGAG RRRRGE

UniProtKB: Sterol regulatory element-binding protein cleavage-activating protein

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Macromolecule #2: Insulin-induced gene protein

MacromoleculeName: Insulin-induced gene protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Molecular weightTheoretical: 24.929936 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEGKTESPG PKRRGPYISS VTSQSVNVVI RGVVLFFIGV FLALVLNLLQ IQRNVTLFPP DVVTSIFSSA WWVPPCCGTA SAVIGLLYP CIDRHLGEPH KFKREWSSVM RCVAVFVGIN HASAKVDFDN NFQFSLTLAA LSVGLWWTFD RSRSGFGLGV G IAFLATVV ...String:
MAEGKTESPG PKRRGPYISS VTSQSVNVVI RGVVLFFIGV FLALVLNLLQ IQRNVTLFPP DVVTSIFSSA WWVPPCCGTA SAVIGLLYP CIDRHLGEPH KFKREWSSVM RCVAVFVGIN HASAKVDFDN NFQFSLTLAA LSVGLWWTFD RSRSGFGLGV G IAFLATVV TQLLVYNGVY QYTSPDFLYV RSWLPCIFFA GGITMGNIGR QLAMYECKVI PEKSHQE

UniProtKB: Insulin-induced gene protein

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Macromolecule #3: Fab4G10 heavy chain

MacromoleculeName: Fab4G10 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.016852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLS SLTSEDTAVY YCTRYNDYDA FYFDYWGQGT TLTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLS SLTSEDTAVY YCTRYNDYDA FYFDYWGQGT TLTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DKTGSGATNF SL LKQAGDV EENPG

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Macromolecule #4: Fab4G10 light chain

MacromoleculeName: Fab4G10 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.545189 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSDIQMT QTTSSLSASL GDRVTISCRA SQDIRNYLNW YQQKPDGTVK LLIYYTSRLH SGVPSRFSGS GSGTDYSLTI SNLEQEDIA TYFCQQTNTL PWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
TGVHSDIQMT QTTSSLSASL GDRVTISCRA SQDIRNYLNW YQQKPDGTVK LLIYYTSRLH SGVPSRFSGS GSGTDYSLTI SNLEQEDIA TYFCQQTNTL PWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE CHHHHHHHHH H

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

7etw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 160849
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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