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- EMDB-72012: Hamster Scap L1-L7 domain/Fab4G10 focused map -

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Basic information

Entry
Database: EMDB / ID: EMD-72012
TitleHamster Scap L1-L7 domain/Fab4G10 focused map
Map data
Sample
  • Complex: Scap bound to Fab4G10
    • Complex: Scap
      • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Complex: Fab4G10
      • Protein or peptide: Fab4G10 heavy chain
      • Protein or peptide: Fab4G10 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordssterol-binding / COPII-binding / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 metabolic process / ER to Golgi transport vesicle membrane ...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 metabolic process / ER to Golgi transport vesicle membrane / protein import into nucleus / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
: / : / 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 ...: / : / 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
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 L1-L7 domain/Fab4G10 focused map
Authors: Williams BC / Kober DL / Bai X / Radhakrishnan A / Rosenbaum DM
History
DepositionAug 7, 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_72012.png

Downloads & links

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Map

FileDownload / File: emd_72012.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 386.928 Å		1.07 Å/pix.
x 360 pix.
= 386.928 Å		1.07 Å/pix.
x 360 pix.
= 386.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0748 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.183
Minimum - Maximum-0.6702308 - 1.4667196
Average (Standard dev.)0.00024138052 (±0.015192724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.928 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_72012_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_72012_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_72012_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 bound to Fab4G10

EntireName: Scap bound to Fab4G10
Components
  • Complex: Scap bound to Fab4G10
    • Complex: Scap
      • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Complex: Fab4G10
      • Protein or peptide: Fab4G10 heavy chain
      • Protein or peptide: Fab4G10 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Scap bound to Fab4G10

SupramoleculeName: Scap bound to Fab4G10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Supramolecule #2: Scap

SupramoleculeName: Scap / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Supramolecule #3: Fab4G10

SupramoleculeName: Fab4G10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Fab4G10 heavy chain

MacromoleculeName: Fab4G10 heavy chain / type: protein_or_peptide / ID: 1 / 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 #2: Fab4G10 light chain

MacromoleculeName: Fab4G10 light chain / type: protein_or_peptide / ID: 2 / 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 #3: Sterol regulatory element-binding protein cleavage-activating protein

MacromoleculeName: Sterol regulatory element-binding protein cleavage-activating protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Molecular weightTheoretical: 144.056594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHT LTERLREKIS QAFYNHGLLC ASYPIPIILF TGLCILACCY PLLKLPLPGT GPVEFSTPVK DYSPPPVDSD HKQGEPSEQ PEWYVGAPVA YIQQIFVKSS VSPWHKNLLA VDVFRLPLSR AFQLVEEIRN HALRDSSGVK SLEEVCLQVT D LLPGLRKL ...String:
MHHHHHHHHT LTERLREKIS QAFYNHGLLC ASYPIPIILF TGLCILACCY PLLKLPLPGT GPVEFSTPVK DYSPPPVDSD HKQGEPSEQ PEWYVGAPVA YIQQIFVKSS VSPWHKNLLA VDVFRLPLSR AFQLVEEIRN HALRDSSGVK SLEEVCLQVT D LLPGLRKL RNLLPEHGCL LLSPGNFWQN DWERFHADPD IIGTIHQHEP KTLQTSATLK DLLFGVPGKY SGVSLYTRKR TV SYTITLV FQRYDSRFLS SLRSRLKLLH PSPNCSLRAE NLVHVHFKEE IGIAELIPLV TTYIILFAYI YFSTRKIDMV KSK WGLALA AVVTVLSSLL MSVGLCTLFG LTPTLNGGEI FPYLVVVIGL ENVLVLTKSV VSTPVDLEVK LRIAQGLSSE SWSI MKNVA TELGIILIGY FTLVPAIQEF CLFAVVGLVS DFFLQMFFFT TVLSIDIRRM ELADLNKRLP PESCLPSAKP VGRPA RYER QLAVRPAMPH TITLQPSSFR NLRLPKRLRV IYFLARTRLA QRLIMAGTVV WIGILVYTDP AGLRTYLAAQ VTEQSP LGE GSLGPMPVPS GVLPASRPDP AFSIFPPDAP KLPENQTVPG ELPEHAAPAE GVHDSRAPEV TWGPEDEELW RRLSFRH WP TLFNYYNITL AKRYISLLPV IPVTLRLNPQ EALEGRQPQD GRSAWAPPES LPAGLWEAGP KGPGGTQAHG DITLYKVA A LGLAAGIVLV LLLLCLYRVL CPRNYGQPGG GAGRRRRGEL PCDDYGYAPP ETEIVPLVLR GHLMDIECLA SDGMLLVSC CLAGQVCVWD AQTGDCLTRI PRPGSRRDSC GGGAFETQEN WERLSDGGKT SPEEPGESPP LRHRPRGPPQ PALFGDQPDL TCLIDTNFS VQLPPEPTQP EPRHRAGCGR ARDSGYDFSR LVQRVYQEEG LAAVRMPALR PPSPGSPLPQ ASQEDGAAPE K GSPPLAWA PSTAGSIWSL ELQGNLIVVG RSSGRLEVWD AIEGVLCCSN EEVSSGITAL VFLDRRIVAA RLNGSLDFFS LE THTSLSP LQFRGTPGRG SSPSSSVYSS SNTVACHLTH TVPCAHQKPI TALRAAAGRL VTGSQDHTLR VFRLEDSCCL FTL QGHSGA ITTVYIDQTM VLASGGQDGA ICLWDVLTGS RVSHTFAHRG DVTSLTCTTS CVISSGLDDL INIWDRSTGI KLYS IQQDL GCGASLGVIS DNLLVTGGQG CVSFWDLNYG DLLQTVYLGK NSEAQPARQI LVLDNAAIVC NFGSELSLVY VPSVL EKLD DYKDDDDKGS DYKDDDDKGS DYKDDDDK

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

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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:

7lkf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 272072
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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