[English] 日本語
Yorodumi
- EMDB-72029: Hamster Scap with bound Fab4G10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72029
TitleHamster Scap with bound Fab4G10
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
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: 3.0 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 with bound Fab4G10
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

-
Structure visualization

Supplemental images

emd_72029.png

Downloads & links

-
Map

FileDownload / File: emd_72029.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: 0.0851
Minimum - Maximum-0.4430346 - 1.1075991
Average (Standard dev.)-0.00020503097 (±0.014233936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.928 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map B

Fileemd_72029_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_72029_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
Supramolecule #1: Scap bound to Fab4G10

SupramoleculeName: Scap bound to Fab4G10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Scap

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

-
Supramolecule #3: Fab4G10

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

-
Macromolecule #1: Fab4G10 heavy chain

MacromoleculeName: Fab4G10 heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLSS LTSEDTAVYY CTRYNDYDAF YFDYWGQGTT LTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA ...String:
TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLSS LTSEDTAVYY CTRYNDYDAF YFDYWGQGTT LTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPKSCDK TGSGATNFSL LKQAGDVEEN PG

-
Macromolecule #2: Fab4G10 light chain

MacromoleculeName: Fab4G10 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSDIQMT QTTSSLSASL GDRVTISCRA SQDIRNYLNW YQQKPDGTVK LLIYYTSRLH SGVPSRFSGS GSGTDYSLTI SNLEQEDIAT YFCQQTNTLP WTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE ...String:
TGVHSDIQMT QTTSSLSASL GDRVTISCRA SQDIRNYLNW YQQKPDGTVK LLIYYTSRLH SGVPSRFSGS GSGTDYSLTI SNLEQEDIAT YFCQQTNTLP WTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGECH HHHHHHHHH

-
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 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHT LTERLREKIS QAFYNHGLLC ASYPIPIILF TGLCILACCY PLLKLPLPGT GPVEFSTPVK DYSPPPVDSD HKQGEPSEQP EWYVGAPVAY IQQIFVKSSV SPWHKNLLAV DVFRLPLSRA FQLVEEIRNH ALRDSSGVKS LEEVCLQVTD LLPGLRKLRN ...String:
MHHHHHHHHT LTERLREKIS QAFYNHGLLC ASYPIPIILF TGLCILACCY PLLKLPLPGT GPVEFSTPVK DYSPPPVDSD HKQGEPSEQP EWYVGAPVAY IQQIFVKSSV SPWHKNLLAV DVFRLPLSRA FQLVEEIRNH ALRDSSGVKS LEEVCLQVTD LLPGLRKLRN LLPEHGCLLL SPGNFWQNDW ERFHADPDII GTIHQHEPKT LQTSATLKDL LFGVPGKYSG VSLYTRKRTV SYTITLVFQR YDSRFLSSLR SRLKLLHPSP NCSLRAENLV HVHFKEEIGI AELIPLVTTY IILFAYIYFS TRKIDMVKSK WGLALAAVVT VLSSLLMSVG LCTLFGLTPT LNGGEIFPYL VVVIGLENVL VLTKSVVSTP VDLEVKLRIA QGLSSESWSI MKNVATELGI ILIGYFTLVP AIQEFCLFAV VGLVSDFFLQ MFFFTTVLSI DIRRMELADL NKRLPPESCL PSAKPVGRPA RYERQLAVRP AMPHTITLQP SSFRNLRLPK RLRVIYFLAR TRLAQRLIMA GTVVWIGILV YTDPAGLRTY LAAQVTEQSP LGEGSLGPMP VPSGVLPASR PDPAFSIFPP DAPKLPENQT VPGELPEHAA PAEGVHDSRA PEVTWGPEDE ELWRRLSFRH WPTLFNYYNI TLAKRYISLL PVIPVTLRLN PQEALEGRQP QDGRSAWAPP ESLPAGLWEA GPKGPGGTQA HGDITLYKVA ALGLAAGIVL VLLLLCLYRV LCPRNYGQPG GGAGRRRRGE LPCDDYGYAP PETEIVPLVL RGHLMDIECL ASDGMLLVSC CLAGQVCVWD AQTGDCLTRI PRPGSRRDSC GGGAFETQEN WERLSDGGKT SPEEPGESPP LRHRPRGPPQ PALFGDQPDL TCLIDTNFSV QLPPEPTQPE PRHRAGCGRA RDSGYDFSRL VQRVYQEEGL AAVRMPALRP PSPGSPLPQA SQEDGAAPEK GSPPLAWAPS TAGSIWSLEL QGNLIVVGRS SGRLEVWDAI EGVLCCSNEE VSSGITALVF LDRRIVAARL NGSLDFFSLE THTSLSPLQF RGTPGRGSSP SSSVYSSSNT VACHLTHTVP CAHQKPITAL RAAAGRLVTG SQDHTLRVFR LEDSCCLFTL QGHSGAITTV YIDQTMVLAS GGQDGAICLW DVLTGSRVSH TFAHRGDVTS LTCTTSCVIS SGLDDLINIW DRSTGIKLYS IQQDLGCGAS LGVISDNLLV TGGQGCVSFW DLNYGDLLQT VYLGKNSEAQ PARQILVLDN AAIVCNFGSE LSLVYVPSVL EKLDDYKDDD DKGSDYKDDD DKGSDYKDDD DK

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

23406

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 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)

+
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