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- EMDB-60523: Cryo-EM Structure of the BLOC-3 complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60523
TitleCryo-EM Structure of the BLOC-3 complex
Map data
Sample
  • Complex: Cryo-EM Structure of the BLOC-3 complex
    • Protein or peptide: BLOC-3 complex member HPS1
    • Protein or peptide: BLOC-3 complex member HPS4
KeywordsRab cascade / Rab GTPase / guanine nucleotide exchange factors / SIGNALING PROTEIN
Function / homology
Function and homology information


BLOC-3 complex / platelet dense granule / positive regulation of eye pigmentation / platelet dense granule organization / melanosome assembly / hemostasis / melanocyte differentiation / RAB GEFs exchange GTP for GDP on RABs / : / lysosome organization ...BLOC-3 complex / platelet dense granule / positive regulation of eye pigmentation / platelet dense granule organization / melanosome assembly / hemostasis / melanocyte differentiation / RAB GEFs exchange GTP for GDP on RABs / : / lysosome organization / intracellular transport / protein targeting / vesicle-mediated transport / visual perception / guanyl-nucleotide exchange factor activity / small GTPase binding / blood coagulation / melanosome / cytoplasmic vesicle / lysosome / protein dimerization activity / protein stabilization / lysosomal membrane / protein homodimerization activity / membrane / cytoplasm / cytosol
Similarity search - Function
BLOC-3 complex member HPS1 / BLOC-3 complex member HPS4 / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 ...BLOC-3 complex member HPS1 / BLOC-3 complex member HPS4 / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1
Similarity search - Domain/homology
BLOC-3 complex member HPS1 / BLOC-3 complex member HPS4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsJia GW / Yong X / Su ZM / Jia D
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 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 BLOC-3 complex
Authors: Jia GW / Yong X / Su ZM / Jia D
History
DepositionJun 12, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60523.png

Downloads & links

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Map

FileDownload / File: emd_60523.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: 0.11
Minimum - Maximum-0.0016312114 - 2.176202
Average (Standard dev.)0.00114755 (±0.02512451)
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_60523_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_60523_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 complex

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

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

SupramoleculeName: Cryo-EM Structure of the BLOC-3 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.376703 KDa
Recombinant expressionOrganism: 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

UniProtKB: BLOC-3 complex member HPS1

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Macromolecule #2: BLOC-3 complex member HPS4

MacromoleculeName: BLOC-3 complex member HPS4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.839996 KDa
Recombinant expressionOrganism: 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

UniProtKB: BLOC-3 complex member HPS4

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 62.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.859 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: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213712
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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