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- EMDB-37498: Cryo-EM structure of GPIb-IX Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37498
TitleCryo-EM structure of GPIb-IX Complex
Map data
Sample
  • Complex: GPIb-IX Complex
    • Protein or peptide: Platelet glycoprotein Ib alpha chain
  • Protein or peptide: Platelet glycoprotein Ib beta chain
  • Protein or peptide: Platelet glycoprotein IX
KeywordsGPIb-IX Complex / platelet / BLOOD CLOTTING
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / release of sequestered calcium ion into cytosol / extracellular matrix / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / platelet activation / blood coagulation / transmembrane signaling receptor activity / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Platelet glycoprotein Ib alpha chain / Platelet glycoprotein Ib beta chain / Platelet glycoprotein IX
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsShu ZM / Duan JS / Zhou AW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-Structure of GPIb-IX complex at 3.36 Angstroms resolution
Authors: Shu ZM / Duan JS / Zhou AW
History
DepositionSep 20, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37498.png

Downloads & links

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Map

FileDownload / File: emd_37498.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 386.712 Å		1.07 Å/pix.
x 360 pix.
= 386.712 Å		1.07 Å/pix.
x 360 pix.
= 386.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0457
Minimum - Maximum-0.018632924 - 2.1327229
Average (Standard dev.)0.00043259907 (±0.015095586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37498_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37498_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 : GPIb-IX Complex

EntireName: GPIb-IX Complex
Components
  • Complex: GPIb-IX Complex
    • Protein or peptide: Platelet glycoprotein Ib alpha chain
  • Protein or peptide: Platelet glycoprotein Ib beta chain
  • Protein or peptide: Platelet glycoprotein IX

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Supramolecule #1: GPIb-IX Complex

SupramoleculeName: GPIb-IX Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Platelet glycoprotein Ib beta chain

MacromoleculeName: Platelet glycoprotein Ib beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.525904 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CPAPCSCAGT LVDCGRRGLT WASLPTAFPV DTTELVLTGN NLTALPPGLL DALPALRTAH LGANPWRCDC RLVPLRAWLA GRPERAPYR DLRCVAPPAL RGRLLPYLAE DELRAACAPG PLCWGALAAQ LALLGLGLLH ALLLVLLLSR LRRLRARARA R AAARLSLT ...String:
CPAPCSCAGT LVDCGRRGLT WASLPTAFPV DTTELVLTGN NLTALPPGLL DALPALRTAH LGANPWRCDC RLVPLRAWLA GRPERAPYR DLRCVAPPAL RGRLLPYLAE DELRAACAPG PLCWGALAAQ LALLGLGLLH ALLLVLLLSR LRRLRARARA R AAARLSLT DPLVAERAGT DESGSGDYKD DDDK

UniProtKB: Platelet glycoprotein Ib beta chain

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Macromolecule #2: Platelet glycoprotein IX

MacromoleculeName: Platelet glycoprotein IX / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.346125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TKDCPSPCTC RALETMGLWV DCRGHGLTAL PALPARTRHL LLANNSLQSV PPGAFDHLPQ LQTLDVTQNP WHCDCSLTYL RLWLEDRTP EALLQVRCAS PSLAAHGPLG RLTGYQLGSC GWQLQASWVR PGVLWDVALV AVAALGLALL AGLLSATTEA L DSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

UniProtKB: Platelet glycoprotein IX

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Macromolecule #3: Platelet glycoprotein Ib alpha chain

MacromoleculeName: Platelet glycoprotein Ib alpha chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.587024 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PDFCCLLPLG FYVLGLFWLL FASVVLILLL SWVGHVKPQA LDSGQGAALT TATQTTHLEL QRGRQVTVPR AWLLFLRGEL PTFRSSLFL WVRPNGRVGP LVAGRRPSAL SQGRGQDLLS TVSIRYSGHE LGGHHHHHHH H

UniProtKB: Platelet glycoprotein Ib alpha chain

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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: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180680
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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