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- EMDB-55103: CryoEM density of NBEAL2 BEACH protein at secondary structure res... -

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Basic information

Entry
Database: EMDB / ID: EMD-55103
TitleCryoEM density of NBEAL2 BEACH protein at secondary structure resolution
Map dataSharpened map
Sample
  • Complex: Neurobeachin-like protein 2 NBEAL2
    • Protein or peptide: Neurobeachin-like protein 2
KeywordsBEACH domain / Gray platelet syndrome / NBEAL1 / NBEAL2 / neurobeachin / LIPID BINDING PROTEIN
Function / homology
Function and homology information


platelet formation / tertiary granule membrane / ficolin-1-rich granule membrane / Neutrophil degranulation / endoplasmic reticulum / membrane / plasma membrane / cytosol
Similarity search - Function
Domain of unknown function (DUF4800) / Neurobeachin/BDCP, DUF4704 / Neurobeachin, beta-propeller domain / Neurobeachin, alpha-solenoid region / : / Neurobeachin/BDCP, DUF4704 alpha solenoid region / Neurobeachin alpha solenoid region / Neurobeachin beta propeller domain / BEACH domain / PH-BEACH domain ...Domain of unknown function (DUF4800) / Neurobeachin/BDCP, DUF4704 / Neurobeachin, beta-propeller domain / Neurobeachin, alpha-solenoid region / : / Neurobeachin/BDCP, DUF4704 alpha solenoid region / Neurobeachin alpha solenoid region / Neurobeachin beta propeller domain / BEACH domain / PH-BEACH domain / BEACH domain superfamily / Beige/BEACH domain / PH domain associated with Beige/BEACH / BEACH domain profile. / BEACH-type PH domain profile. / Beige/BEACH domain / Armadillo-like helical / PH-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold / 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
Neurobeachin-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsMann D / Dahl AK / Sachse C / Simonsen A / Pankiv S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: J Cell Biol / Year: 2026
Title: Characterizing the membrane recruitment domain of BDCPs and its role in gray platelet syndrome.
Authors: Anette Kathinka Dahl / Daniel Mann / Alf Håkon Lystad / Carsten Sachse / Anne Simonsen / Serhiy Pankiv /
Abstract: BEACH domain-containing proteins (BDCPs) represent a family of large membrane-associated transmembrane cargo adaptors. In the current study, we determined the cryo-EM structure of the full-length ...BEACH domain-containing proteins (BDCPs) represent a family of large membrane-associated transmembrane cargo adaptors. In the current study, we determined the cryo-EM structure of the full-length typical BDCP NBEAL2, revealing an N-terminal arch-like structure with C-terminal globular domains attached to its convex surface. Using structure-guided deletion mutants and protein chimeras as well as native alternatively spliced isoforms and disease-related point mutants, we show that the N-terminal α-solenoid/concanavalin A-like domain assembly of the typical BDCPs NBEAL1, NBEAL2, LYST, ALFY, LRBA, and NBEA functions as a modular membrane recruitment domain. We report that gray platelet syndrome-associated single aa mutations L388P or E643V within the membrane recruitment domain of NBEAL2 disrupt its membrane targeting in stably transfected cells, highlighting a potential structure-function mechanism by which failed membrane recruitment cause gray platelet syndrome or other BDCPs-related diseases.
History
DepositionSep 18, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55103.png

Downloads & links

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Map

FileDownload / File: emd_55103.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 256 pix.
= 417.28 Å		1.63 Å/pix.
x 256 pix.
= 417.28 Å		1.63 Å/pix.
x 256 pix.
= 417.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.7600759 - 2.0938878
Average (Standard dev.)-0.0012777038 (±0.047542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 417.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55103_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local resolution map

Fileemd_55103_additional_1.map
Annotationlocal resolution map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local resolution filtered map

Fileemd_55103_additional_2.map
Annotationlocal resolution filtered map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_55103_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_55103_half_map_2.map
Annotationhalf map B
Projections & Slices
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Sample components

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Entire : Neurobeachin-like protein 2 NBEAL2

EntireName: Neurobeachin-like protein 2 NBEAL2
Components
  • Complex: Neurobeachin-like protein 2 NBEAL2
    • Protein or peptide: Neurobeachin-like protein 2

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Supramolecule #1: Neurobeachin-like protein 2 NBEAL2

SupramoleculeName: Neurobeachin-like protein 2 NBEAL2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 302.517 KDa

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Macromolecule #1: Neurobeachin-like protein 2

MacromoleculeName: Neurobeachin-like protein 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAASERLYEL WLLYYAQKDL GYLQQWLKAF VGAFKKSISL SSLEPRRPEE AGAEVPLLPL DELHVLAEQL HQADLEQALL LLKLFIILCR NLENIEAGRG QVLVPRVLAL LTKLVAELKG CPPPQGRGTQ LENVALHALL LCEGLFDPYQ TWRRQRSGEV ISSKEKSKYK ...String:
MAASERLYEL WLLYYAQKDL GYLQQWLKAF VGAFKKSISL SSLEPRRPEE AGAEVPLLPL DELHVLAEQL HQADLEQALL LLKLFIILCR NLENIEAGRG QVLVPRVLAL LTKLVAELKG CPPPQGRGTQ LENVALHALL LCEGLFDPYQ TWRRQRSGEV ISSKEKSKYK FPPAALPQEF SAFFQESLQN ADHLPPILLL RLIHLFCAVL AGGKENGQMA VSDGSVKGLL SVVRGWSRGP APDPCLVPLA LEALVGAVHV LHASRAPPRG PELRALLESY FHVLNADWPA GLSSGPEEAL VTLRVSMLDA IPMMLACEDR PVLQATFLSN NCFEHLTRLI QNSKLYLQSR APPEGDSDLA TRLLTEPDVQ KVLDQDTDAI AVHVVRVLTC IMSDSPSAKE VFKERIGYPH LQEVLQSHGP PTHRLLQELL NMAVEGDHSM CPPPPIRNEQ PVLVLAQWLP SLPTAELRLF LAQRLRWLCD SCPASRATCV QAGLVGCLLE TLSTGLALEA RCQEQLLALL QALGRVSIRP MELRHLLRPR PGLDSEPGGA EAGKARHAGA VIRTLSGMAR HQGPARALRY FDLTPSMAGI MVPPVQRWPG PGFTFHAWLC LHPMDTAPTP APTRPLQRKQ LYSFFTSSGS GFEAFFTAAG TLVVAVCTRK EYLTMSLPEV SFADSAWHCV AIVHVPGRRP FSQNLVHVYK DGHLVKTAPL RCPSLSEPFS SCCIGSAGYR TTTTTTGLPT PPVPATLAYT HPALTRSQSV PASTGLGWGS GLVAPLQEGS IDSTLAGTQD TRWGSPTSLE GELGAVAIFH EALQATALRT LCTLGPNETA PFKPEGELHE LSTRLLLHYS PQACKNNICL DLSPSHGLDG RLTGHRVETW DVKDVVNCVG GMGALLPLLE RVAAQPKEAE AGPAETHDLV GPELTSGHNT QGLVLPLGKS SEERMERNAV AAFLLMLRNF LQGHMVNQES LVQCQGPAII GALLRKVPSW AMDMNVLMSA QLLMEQVAAE GSGPLLYLLY QHLLFNFHLW TLSDFAVRLG HIQYMSSIVR EHRQKLRKKY GVQFILDALR THYSPQRERP LAADDLRTVQ TSLLGLAREF LVRSLSADDV QVTQTMLSFL AATGDDGQAV GALDLLLALL HGSLVQESLA VFLLEPGNLE VLLALLVRPG SLPLLPDRVC KILRRLQQNE RLPERSRQRL RLRECGLQGL VACLPEGTVS PQLCQGLYKL FLGADCLNLS DLLAVVQLSL QADLSVRLDI CRQLFHLIYG QPDVVRLLAR QAGWQDVLTR LYVLEAATAG SPPPSSPESP TSPKPAPPKP PTESPAEPSD VFLPSEAPCP DPDGFYHALS PFCTPFDLGL ERSSVGSGNT AGGGGSSGTL TPASQPGTPS PLDGPRPFPA APGRHSSSLS NVLEDGSLPE PTISGDDTSN TSNPQQTSEE ELCNLLTNVL FSVTWRGVEG SDEAAWRERG QVFSVLTQLG ASATLVRPPD CIKRSLLEMM LESALTDIKE APVGVLASLT QQALWLLRLL QDFLCAEGHG NQELWSEKLF EGVCSLLDRL GAWPHLANGT ADLREMAQIG LRLVLGYILL EDPQLHAQAY VRLHMLLQTA VPARREEACY VLSKLEAALG RVLNTSSLES ATDEAGSPLA AAAAAAAAER CSWLVPLVRT LLDRAYEPLG LQWGLPSLPP TNGSPTFFED FQAFCATPEW RHFIDKQVQP TMSQFEMDTY AKSHDLMSGF WNACYDMLMS SGQRRQWERA QSRRAFQELV LEPAQRRARL EGLRYTAVLK QQATQHSMAL LHWGALWRQL ASPCGAWALR DTPIPRWKLS SAETYSRMRL KLVPNHHFDP HLEASALRDN LGEVPLTPTE EASLPLAVTK EAKVSTPPEL LQEDQLGEDE LAELETPMEA AELDEQREKL VLSAECQLVT VVAVVPGLLE VTTQNVYFYD GSTERVETEE GIGYDFRRPL AQLREVHLRR FNLRRSALEL FFIDQANYFL NFPCKVGTTP VSSPSQTPRP QPGPIPPHTQ VRNQVYSWLL RLRPPSQGYL SSRSPQEMLR ASGLTQKWVQ REISNFEYLM QLNTIAGRTY NDLSQYPVFP WVLQDYVSPT LDLSNPAVFR DLSKPIGVVN PKHAQLVREK YESFEDPAGT IDKFHYGTHY SNAAGVMHYL IRVEPFTSLH VQLQSGRFDC SDRQFHSVAA AWQARLESPA DVKELIPEFF YFPDFLENQN GFDLGCLQLT NEKVGDVVLP PWASSPEDFI QQHRQALESE YVSAHLHEWI DLIFGYKQRG PAAEEALNVF YYCTYEGAVD LDHVTDERER KALEGIISNF GQTPCQLLKE PHPTRLSAEE AAHRLARLDT NSPSIFQHLD ELKAFFAEVV SDGVPLVLAL VPHRQPHSFI TQGSPDLLVT VSASGLLGTH SWLPYDRNIS NYFSFSKDPT MGSHKTQRLL SGPWVPGSGV SGQALAVAPD GKLLFSGGHW DGSLRVTALP RGKLLSQLSC HLDVVTCLAL DTCGIYLISG SRDTTCMVWR LLHQGGLSVG LAPKPVQVLY GHGAAVSCVA ISTELDMAVS GSEDGTVIIH TVRRGQFVAA LRPLGATFPG PIFHLALGSE GQIVVQSSAW ERPGAQVTYS LHLYSVNGKL RASLPLAEQP TALTVTEDFV LLGTAQCALH ILQLNTLLPA APPLPMKVAI RSVAVTKERS HVLVGLEDGK LIVVVAGQPS EVRSSQFARK LWRSSRRISQ VSSGETEYNP TEAR

UniProtKB: Neurobeachin-like protein 2

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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

Concentration0.3 mg/mL
BufferpH: 8.6
Component:
ConcentrationFormulaName
50.0 mMTrisTris
150.0 mMNaClsodium chloride
1.0 mMDTTDTT

Details: 50 mM Tris pH 8.6, 150 mM NaCl, Protease inhibitor cocktail, 1 mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Details: Pelco EasiGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blotforce -5, 3.6 microliter sample volume, 3x application (multiple blot).

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 14003 / Average electron dose: 70.0 e/Å2 / Details: CDS super-resolution counting mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionDetails: template matching
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Details: patch ctf estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio 3D
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 27600
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1) / Details: homogeneous refinement, local refinement
FSC plot (resolution estimation)

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