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전자현미경 데이터
생쥐 ABCB9 단백질의 초저온 전자현미경 구조
  • Accession
    KIX10047732
  • Submission date
    2026-02-13
Project Detail
Dataset detail - Accession, 프로젝트의 영문 제목, 프로젝트의 국문 제목, 프로젝트의 영문 설명, 프로젝트의 국문 설명
Accession
 KAP242249
프로젝트의 영문 제목
Time-resolved cryo-EM study of ABC transporters
프로젝트의 국문 제목
시간 분해능 cryo-EM을 이용한 ABC 트랜스포터 구조 전이 연구
프로젝트의 영문 설명
Humans have a total of 48 ABC transporters, which share a common mechanism of ATP hydrolysis–driven transport to move diverse substrates across cellular membranes. Mutations and functional defects in these transporters are major causes of a wide range of intractable diseases, including cancer, metabolic disorders, immune and neurological diseases. Despite their biological and clinical importance, structural studies of ABC transporters have historically focused mainly on bacterial homologs, largely because large-scale production and crystallization of eukaryotic membrane proteins are technically challenging. In this study, we will use cryo-electron microscopy (cryo-EM) to determine high-resolution structures of eukaryotic ABC transporters and to elucidate the molecular mechanism associated with ATP hydrolysis and substrate transport with millisecond time resolution.
프로젝트의 국문 설명
인간에게는 총 48개의 ABC 트랜스포터가 있으며, 공통적으로 ATP를 가수분해하여 다양한 기질을 세포막 내외로 운반함. 이들의 돌연변이 및 기능 이상은 다양한 난치성 질환 (암, 대사, 면역, 뇌신경 질환)의 주요 원인임. 이러한 생물학적 중요성에도 불구하고 대량생산 및 결정 생성의 어려움으로 인하여 현재까지의 ABC 트랜스포터 구조연구는 대부분 박테리아 유사 단백질에 집중되어 왔으며, 인간 트랜스포터의 구조연구는 극히 일부만 성공하였음. 본 연구에서는 cryo-EM을 이용하여 인간 ABC 트랜스포터의 고해상도 분자입체구조를 규명하고, ATP 가수분해 및 기질 수송으로 인한 ABC 트랜스포터의 구조 및 구조 전이 과정을 밀리초 (millisecond) 시간 분해능으로 규명하고자 함.
메타데이터 정보
메타데이터 입력
장비 유형
TEM
Name
진미선
Email address
misunjin@gist.ac.kr
Role assignment
Principal investgator
Contributor
Contributor name
Contributor email
Contributor role assignment
Contributor role notation
typeOfInstrument
TEM
Representative image data file
Title - English
Cryo-EM structure of the mouse ABCB9 (ADP.BeF3-bound)
Title - Korean
생쥐 ABCB9 단백질의 초저온 전자현미경 구조
Experimental method
Single particle analysis
Raw Data
Data upload
Pixel size
Pixel size
Pixel units
Accelerating Voltage
Working distance
Emission current
Signal type
Stage temperature
Map data
Map data
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Annotated data upload
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
Raw Data
Data upload
Pixel size For Data upload
Pixel size
Pixel units
Stage Tilt
Tilt angle (alpha axis)
Tilt angle (beta axis)
EMPIAR ID
Description of the raw data
Map data
Annotated data
Select raw data
Annotated data upload
Description of the annotated data
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
Raw Data
Data upload
Data upload
Pixel size
Pixel size
0.83
Pixel units
Å
Select the raw data type of SPA
Raw multiframe(raw movies)
Stage Tilt
Tilt angle (alpha axis)
Tilt angle (beta axis)
EMPIAR ID
Web database deposition ID
Enter EMDB ID
EMD-31722
Enter PDB ID
7V5C
Description of input data
Map data
Yes
Map data
Upload map data
Pixel size
Pixel size
0.83
Pixel units
Å
Select the map data type
Unsharpened map
Recommended contour level
Resolution at 0.143 FSC
Applied symmetry
Software for reconstruction
Other database id
Enter EMDB ID
Enter PDB ID
Description of map data
Raw Data
Other types of raw data
Data upload
Pixel size
Pixel size
Pixel units
Select the raw data type of SPA
Stage Tilt
Tilt angle (alpha axis)
Tilt angle (beta axis)
EMPIAR ID
Web database deposition ID
Enter EMDB ID
Enter PDB ID
Description of input data
Map data
Map data
Upload map data
Pixel size
Pixel size
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Recommended contour level
Resolution at 0.143 FSC
Helical parameter
Rise value of helical parameter
Twist value of helical parameter
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Enter EMDB ID
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Description of map data
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Tilt series
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EMPIAR ID
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Enter EMDB ID
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Upload tomogram
Pixel size
Pixel size
Pixel units
Software for reconstruction
Description of tomogram data
Upload labeled data
Pixel size
Pixel size
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Software for segmentation
Description of labeled data
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
Raw Data
Upload averaged 3D map data
Pixel size
Pixel size
Pixel units
Recommended contour level
Resolution at 0.143 FSC
Applied symmetry
Software for refinement
Upload raw tilt series
Pixel size
Pixel size
Pixel units
EMPIAR ID
Web database deposition ID
Enter EMDB ID
Enter PDB ID
Description of input data
Annotated data
Select raw data
Tilt series
Minimum angle
Maximum angle
Angle imcrement
Excluded views
Or write manually
Tilt axis (image rotation)
Add fiducial markers
Description of tilt series
Upload tomogram
Pixel size
Pixel size
Pixel units
Software for reconstruction
Description of tomogram data
Upload subtomograms
Pixel size
Pixel size
Pixel units
Upload labeled data
Pixel size
Pixel size
Pixel units
Software for segmentation
Description of labeled data
Light micrograph for CLEM
Light micrograph data upload
Light micrograph - Manufacturer and model
Light source type
Objective Magnification
Optical section (Z)
Optical section (Z) thickness
Timelapse (T)
Timelapse (T) fps
Information for channels and target molecules
Data type
Process information
Image format
Image analysis program
Description of the light micrograph for CLEM
typeOfInstrument
TEM
Category
Sample name
Scientific name
Natural source- Taxonomy ID (NCBI)
Sample Description
Category
Select raw data
Sample type
Sample name
Scientific name
Natural source- Taxonomy ID (NCBI)
Strain
Sample Description
Category
Select raw data
image.png,image.png,image.png
Sample type
Protein etc.
Protein
Protein name
ABCB9
Number of copies
2
Recombinant protein sequence
Recombinant protein sequence
MRLWKAVVVT LAFVSTDVGV TTAIYAFSHL DRSLLEDIRH FNIFDSVLDL WAACLYRSCL LLGATIGVAK NSALGPRRLR ASWLVITLVCLFVGIYAMAK LLLFSEVRRP IRDPWFWALF VWTYISLAAS FLLWGLLATV RPDAEALEPG NEGFHGEGGA PAEQASGATL QKLLSYTKPDVAFLVAASFF LIVAALGETF LPYYTGRAID SIVIQKSMDQ FTTAVVVVCL LAIGSSLAAG IRGGIFTLVF ARLNIRLRNC LFRSLVSQETSFFDENRTGD LISRLTSDTT MVSDLVSQNI NIFLRNTVKV TGVVVFMFSL SWQLSLVTFM GFPIIMMVSN IYGKYYKRLS KEVQSALARASTTAEETISA MKTVRSFANE EEEAEVFLRK LQQVYKLNRK EAAAYMSYVW GSGLTLLVVQ VSILYYGGHL VISGQMSSGN LIAFIIYEFVLGDCMESVGS VYSGLMQGVG AAEKVFEFID RQPTMVHDGS LAPDHLEGRV DFENVTFTYR TRPHTQVLQN VSFSLSPGKV TALVGPSGSGKSSCVNILEN FYPLQGGRVL LDGKPIGAYD HKYLHRVISL VSQEPVLFAR SITDNISYGL PTVPFEMVVE AAQKANAHGF IMELQDGYSTETGEKGAQLS GGQKQRVAMA RALVRNPPVL ILDEATSALD AESEYLIQQA IHGNLQRHTV LIIAHRLSTV ERAHLIVVLD KGRVVQQGTHQQLLAQGGLY AKLVQRQMLG LEHPLDYTAS HKEPPSNTEH KA
Description of recombinant protein sequence
MRLWKAVVVTLAFVSTDVGVTTAIYAFSHLDRSLLEDIRHFNIFDSVLDLWAACLYRSCLLLGATIGVAKNSALGPRRLRASWLVITLVCLFVGIYAMAKLLLFSEVRRPIRDPWFWALFVWTYISLAASFLLWGLLATVRPDAEALEPGNEGFHGEGGAPAEQASGATLQKLLSYTKPDVAFLVAASFFLIVAALGETFLPYYTGRAIDSIVIQKSMDQFTTAVVVVCLLAIGSSLAAGIRGGIFTLVFARLNIRLRNCLFRSLVSQETSFFDENRTGDLISRLTSDTTMVSDLVSQNINIFLRNTVKVTGVVVFMFSLSWQLSLVTFMGFPIIMMVSNIYGKYYKRLSKEVQSALARASTTAEETISAMKTVRSFANEEEEAEVFLRKLQQVYKLNRKEAAAYMSYVWGSGLTLLVVQVSILYYGGHLVISGQMSSGNLIAFIIYEFVLGDCMESVGSVYSGLMQGVGAAEKVFEFIDRQPTMVHDGSLAPDHLEGRVDFENVTFTYRTRPHTQVLQNVSFSLSPGKVTALVGPSGSGKSSCVNILENFYPLQGGRVLLDGKPIGAYDHKYLHRVISLVSQEPVLFARSITDNISYGLPTVPFEMVVEAAQKANAHGFIMELQDGYSTETGEKGAQLSGGQKQRVAMARALVRNPPVLILDEATSALDAESEYLIQQAIHGNLQRHTVLIIAHRLSTVERAHLIVVLDKGRVVQQGTHQQLLAQGGLYAKLVQRQMLGLEHPLDYTASHKEPPSNTEHKA
Total molecular weight of all identical protomers
169.13 kDa
Natural source
Scientific name
Mus musculus
Natural source- Taxonomy ID (NCBI)
10090
Strain
Mus musculus
Expression source
Natural source와 다름
Protein
Organism used for expression
Spodoptera frugiperda
NCBI Taxonomy ID of expression source
7108
Cell strain of expression source
Ligand
Name of ligand
Description of ligand
Nucleic acid
Nucleic acid sequence
Description of nucleic acid
Natural source- Sample Description
Name
Scientific Name
Natural source- Taxonomy ID (NCBI)
Sample Description
Type of sample preparation method
Vitrification(for cryo-EM)
Sample preparation method information
Type of fixation
Fixation Infomation
Fixation description
Pre-staining solution formulation
Description of pre-staining procedure
Embedding resin
Resin mixture formulation
Ultra-thin section type
Thickness of section
Depth of serial section
Post-staining solution formulation
Description of post-staining method
Immuno-labeling
Immuno labeling object for fixation
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Fixation Infomation
Vitrification method
Equipment model name for Plunge freezing
Description of Plunge freezing
Equipment model name for high pressure freezing
Cryoprotectant for high pressure freezing
Description of high pressure freezing
Ultramicrotome Type
Equipment name for freeze substitution
Description of freeze substitution
Embedding resin
Resin mixture formulation
Ultra-thin section type
Thickness of section
Depth of serial section
Post-staining solution formulation
Description of post-staining method
Immuno-labeling
Immuno labeling
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sample preparation method information
Concentration of sample used
Sample concentration
Unit
Applied sample volume
Staining solution
Description of staining
Grid Manufacturer
Grid type
Glow discharge applied
Surface polarity
Surface charge
Atmosphere
Immuno-labeling
Immuno labeling object for fixation
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sample preparation method information
Vitrification method
Plunge freezing
Vitrification information
Concentration of sample used
Sample concentration
0.46 ~ 5
Unit
mg/mL
Applied sample volume
Plunge freezer manufacturer
Plunge freezer model
Grid Manufacturer
Grid type
Glow discharge applied
Yes
Surface polarity
Hydrophillic
Surface charge
Negative
Atmosphere
air
Description of vitrification
Immuno-labeling
No
Immuno labeling object for vitrification
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Vitrification information
Method name
Concentration of sample used
Sample concentration
Unit
Applied sample volume
Plunge freezer manufacturer
Plunge freezer model
Grid Manufacturer
Grid type
Glow discharge applied
Surface polarity
Surface charge
Atmosphere
Description of vitrification
Immuno-labeling
Immuno labeling object for vitrification
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sample preparation method information
Method name
Description of method
Immuno Labeling
Immuno-labeling method
Experiment condition
Labeling method
1st Antibody
Pimary antibody
Conjugated material of Primary antibody
Diameter of conjugated material
2nd Antibody
Secondary antibody
Conjugated material of Secondary antibody
Diameter of conjugated material
Description of immunostaining procedure
Sputtering
Coat target
Discharge current
Deposition time
Description of sputtering
typeOfInstrument
TEM
typeOfInstrument
TEM
Site
Site of data collection
IMP, POSTECH
Site Address
Imaging Instrument - Manufacturer
Thermo Fisher Scientific(FEI)
Imaging Instrument - Model
Talos Arctica
Beam Source - Accelerating Voltage
200 kV
Detector - Manufacturer
GATAN
Instrument - Model
BioQuantum K3
Imaging mode
Bright field
Defocus range
Min
Max
Gun type
Gun type
Thermonic emission type
Filed emission type
Related data
KBI
  • 전자현미경 데이터
    2

K-BDS 바이오이미지 데이터는 과학적 조사, 교육, 연구 계획을 목적으로 하는 사용자에게 데이터에 대한 액세스를 제공되며, 데이터의 상업적 이용은 불가합니다.
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