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- EMDB-62821: Cryo-EM Structure of the BLOC-3-RAB9A complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62821
TitleCryo-EM Structure of the BLOC-3-RAB9A complex
Map data
Sample
  • Complex: Cryo-EM Structure of the BLOC-3-RAB9A complex
    • Protein or peptide: BLOC-3 complex member HPS1
    • Protein or peptide: BLOC-3 complex member HPS4
    • Protein or peptide: RAB9A
KeywordsRab cascade / Rab GTPase / guanine nucleotide exchange factors / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsJia GW / Yong X / Su ZM / Jia D
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)32222040 China
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
CitationJournal: To Be Published
Title: Cryo-EM Structure of the BLOC-3-RAB9A complex
Authors: Jia GW / Yong X / Su ZM / Jia D
History
DepositionDec 21, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62821.png

Downloads & links

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Map

FileDownload / File: emd_62821.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0669
Minimum - Maximum-0.0016431249 - 2.6336844
Average (Standard dev.)0.0013490064 (±0.02649716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62821_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_62821_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 : Cryo-EM Structure of the BLOC-3-RAB9A complex

EntireName: Cryo-EM Structure of the BLOC-3-RAB9A complex
Components
  • Complex: Cryo-EM Structure of the BLOC-3-RAB9A complex
    • Protein or peptide: BLOC-3 complex member HPS1
    • Protein or peptide: BLOC-3 complex member HPS4
    • Protein or peptide: RAB9A

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Supramolecule #1: Cryo-EM Structure of the BLOC-3-RAB9A complex

SupramoleculeName: Cryo-EM Structure of the BLOC-3-RAB9A complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BLOC-3 complex member HPS1

MacromoleculeName: BLOC-3 complex member HPS1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MKCVLVATEG AEVLFYWTDQ EFEESLRLKF GQSENEEEEL PALEDQLSTL LAPVIISSMT MLEKLSDTYT CFSTENGNFL YVLHLFGEC LFIAINGDHT ESEGDLRRKL YVLKYLFEVH FGLVTVDGHL IRKELRPPDL AQRVQLWEHF QSLLWTYSRL R EQEQCFAV ...String:
MKCVLVATEG AEVLFYWTDQ EFEESLRLKF GQSENEEEEL PALEDQLSTL LAPVIISSMT MLEKLSDTYT CFSTENGNFL YVLHLFGEC LFIAINGDHT ESEGDLRRKL YVLKYLFEVH FGLVTVDGHL IRKELRPPDL AQRVQLWEHF QSLLWTYSRL R EQEQCFAV EALERLIHPQ LCELCIEALE RHVIQAVNTS PERGGEEALH AFLLVHSKLL AFYSSHSASS LRPADLLALI LL VQDLYPS ESTAEDDIQP SPRRARSSQN IPVQQAWSPH STGPTGGSSA ETETDSFSLP EEYFTPAPSP GDQSSGSTIW LEG GTPPMD ALQIAEDTLQ TLVPHCPVPS GPRRIFLDAN VKESYCPLVP HTMYCLPLWQ GINLVLLTRS PSAPLALVLS QLMD GFSML EKKLKEGPEP GASLRSQPLV GDLRQRMDKF VKNRGAQEIQ STWLEFKAKA FSKSEPGSSW ELLQACGKLK RQLCA IYRL NFLTTAPSRG GPHLPQHLQD QVQRLMREKL TDWKDFLLVK SRRNITMVSY LEDFPGLVHF IYVDRTTGQM VAPSLN CSQ KTSSELGKGP LAAFVKTKVW SLIQLARRYL QKGYTTLLFQ EGDFYCSYFL WFENDMGYKL QMIEVPVLSD DSVPIGM LG GDYYRKLLRY YSKNRPTEAV RCYELLALHL SVIPTDLLVQ QAGQLARRLW EASRIPLL

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Macromolecule #2: BLOC-3 complex member HPS4

MacromoleculeName: BLOC-3 complex member HPS4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GSMATSTSTE AKSASWWNYF FLYDGSKVKE EGDPTRAGIC YFYPSQTLLD QQELLCGQIA GVVRCVSDIS DSPPTLVRLR KLKFAIKVD GDYLWVLGCA VELPDVSCKR FLDQLVGFFN FYNGPVSLAY ENCSQEELST EWDTFIEQIL KNTSDLHKIF N SLWNLDQT ...String:
GSMATSTSTE AKSASWWNYF FLYDGSKVKE EGDPTRAGIC YFYPSQTLLD QQELLCGQIA GVVRCVSDIS DSPPTLVRLR KLKFAIKVD GDYLWVLGCA VELPDVSCKR FLDQLVGFFN FYNGPVSLAY ENCSQEELST EWDTFIEQIL KNTSDLHKIF N SLWNLDQT KVEPLLLLKA ARILQTCQRS PHILAGCILY KGLIVSTQLP PSLTAKVLLH RTAPQEQRLP TGEDAPQEHG AA LPPNVQI IPVFVTKEEA ISLHEFPVEQ MTRSLASPAG LQDGSAQHHP KGGGPSADGI SSRLTPAESC MGLVRMNLYT HCV KGLVLS LLAEEPLLGD SAAIEEVYHS SLASLNGLEV HLKETLPRDE AASTSSTYNF THYDRIQSLL MANLPQVATP QDRR FLQAV SLMHSEFAQL PALYEMTVRN ASTAVYACCN PIQETYFQQL APAARSSGFP NPQDGAFSLS GKAKQKLLKH GVNLL

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Macromolecule #3: RAB9A

MacromoleculeName: RAB9A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHHHH HENLYFGQMA GKSSLFKVIL LGDGGVGKSS LMNRYVTNKF DTQLFHTIGV EFLNKDLEVD GHFVTMQIWD TAGQERFRSL RTPFYRGSDC CLLTFSVDDS QSFQNLSNWK KEFIYYADVK EPESFPFVIL GNKIDISERQ VSTEEAQAWC RDNGDYPYFE ...String:
MHHHHHHHHH HENLYFGQMA GKSSLFKVIL LGDGGVGKSS LMNRYVTNKF DTQLFHTIGV EFLNKDLEVD GHFVTMQIWD TAGQERFRSL RTPFYRGSDC CLLTFSVDDS QSFQNLSNWK KEFIYYADVK EPESFPFVIL GNKIDISERQ VSTEEAQAWC RDNGDYPYFE TSAKDATNVA AAFEEAVRRV LATEDRSDHL IQTDTVNLHR KPKPSSSCC

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 61.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93089
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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