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- PDB-9la9: Munc13-4-Rab27a complex with GppNHp -

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Basic information

Entry
Database: PDB / ID: 9la9
TitleMunc13-4-Rab27a complex with GppNHp
Components
  • Protein unc-13 homolog D
  • Ras-related protein Rab-27A
KeywordsEXOCYTOSIS / Vesicle tethering / Familial hemophagocytic lymphohistiocytosis type 3 /FHL3 / Griscelli syndrome type 2 /GS2
Function / homology
Function and homology information


multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / granuloma formation / melanosome localization / natural killer cell degranulation / exosomal secretion / regulation of mast cell degranulation / Weibel-Palade body ...multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / granuloma formation / melanosome localization / natural killer cell degranulation / exosomal secretion / regulation of mast cell degranulation / Weibel-Palade body / exocytic vesicle / multivesicular body sorting pathway / melanocyte differentiation / myosin V binding / RAB geranylgeranylation / melanosome membrane / melanosome transport / multivesicular body membrane / RAB GEFs exchange GTP for GDP on RABs / complement-dependent cytotoxicity / germinal center formation / Insulin processing / synaptic vesicle transport / antigen processing and presentation / positive regulation of reactive oxygen species biosynthetic process / Regulation of MITF-M-dependent genes involved in pigmentation / exocytosis / positive regulation of exocytosis / protein secretion / photoreceptor outer segment / phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / secretion / positive regulation of phagocytosis / secretory granule / small monomeric GTPase / recycling endosome / small GTPase binding / specific granule lumen / blood coagulation / GDP binding / azurophil granule lumen / melanosome / late endosome / G protein activity / defense response to virus / lysosome / apical plasma membrane / protein domain specific binding / intracellular membrane-bounded organelle / GTPase activity / dendrite / Neutrophil degranulation / positive regulation of gene expression / GTP binding / Golgi apparatus / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
: / Rab27a/b / Mammalian uncoordinated homology 13, domain 2 / Munc13-homology domain 2 (MHD2) profile. / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / : / Small GTPase Rab domain profile. ...: / Rab27a/b / Mammalian uncoordinated homology 13, domain 2 / Munc13-homology domain 2 (MHD2) profile. / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / : / Small GTPase Rab domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-27A / Protein unc-13 homolog D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.38 Å
AuthorsZheng, X. / Liu, C.Q. / Wang, S. / Guan, J.L. / He, J. / Ma, C.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32225024, 92254302 China
National Natural Science Foundation of China (NSFC)2022YFA1206001 China
National Natural Science Foundation of China (NSFC)32241021 China
National Natural Science Foundation of China (NSFC)32170189 China
National Natural Science Foundation of China (NSFC)3231163669 China
Other private2024A04J6348
CitationJournal: Nat Commun / Year: 2025
Title: Munc13-4 mediates tumor immune evasion by regulating the sorting and secretion of PD-L1 via exosomes
Authors: Liu, C.Q. / Liu, D.X. / Zheng, X. / Guan, J.L. / Zhou, X.Y. / Zhang, H.K. / Wang, S. / Li, Q.B. / Gan, L. / He, J. / Ma, C.
History
DepositionJan 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein unc-13 homolog D
B: Ras-related protein Rab-27A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,8583
Polymers156,3362
Non-polymers5221
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein unc-13 homolog D / Munc13-4


Mass: 126816.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNC13D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q70J99
#2: Protein Ras-related protein Rab-27A / Rab-27 / GTP-binding protein Ram


Mass: 29520.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB27A, RAB27 / Production host: Escherichia coli (E. coli) / References: UniProt: P51159, small monomeric GTPase
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Munc13-4-Rab27a complex with GppNHpCOMPLEX#1-#20RECOMBINANT
2Munc13-4COMPLEX#21RECOMBINANT
3Rab27aCOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Escherichia coli (E. coli)562
Buffer solutionpH: 8.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102381 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 4.38 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059430
ELECTRON MICROSCOPYf_angle_d0.94512785
ELECTRON MICROSCOPYf_dihedral_angle_d5.7731253
ELECTRON MICROSCOPYf_chiral_restr0.051443
ELECTRON MICROSCOPYf_plane_restr0.0071662

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