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- EMDB-32622: Cryo-EM structure of VWF D'D3 dimer (R1136M/E1143M mutant) comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-32622
TitleCryo-EM structure of VWF D'D3 dimer (R1136M/E1143M mutant) complexed with D1D2 at 3.29 angstron resolution (2 units)
Map data
Sample
  • Complex: VWF D'D3-D1D2 complex (1 unit)
    • Protein or peptide: von Willebrand antigen 2
    • Protein or peptide: von Willebrand factor
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / Platelet Adhesion to exposed collagen / platelet alpha granule / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / immunoglobulin binding ...Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / Platelet Adhesion to exposed collagen / platelet alpha granule / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / immunoglobulin binding / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / Integrin signaling / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsZeng JW / Shu ZM / Zhou AW
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
CitationJournal: Cell Discov / Year: 2022
Title: Structural mechanism of VWF D'D3 dimer formation.
Authors: Zimei Shu / Jianwei Zeng / Li Xia / Haiyan Cai / Aiwu Zhou /
History
DepositionJan 17, 2022-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32622.png

Downloads & links

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Map

FileDownload / File: emd_32622.map.gz / Format: CCP4 / Size: 49.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.97 Å
Density
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.023236403 - 0.04649112
Average (Standard dev.)0.0005484473 (±0.0024051005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions281201231
Spacing201281231
CellA: 194.97 Å / B: 272.57 Å / C: 224.07 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : VWF D'D3-D1D2 complex (1 unit)

EntireName: VWF D'D3-D1D2 complex (1 unit)
Components
  • Complex: VWF D'D3-D1D2 complex (1 unit)
    • Protein or peptide: von Willebrand antigen 2
    • Protein or peptide: von Willebrand factor
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: VWF D'D3-D1D2 complex (1 unit)

SupramoleculeName: VWF D'D3-D1D2 complex (1 unit) / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: von Willebrand antigen 2

MacromoleculeName: von Willebrand antigen 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.427703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEGTRGRSST ARCSLFGSDF VNTFDGSMYS FAGYCSYLLA GGCQKRSFSI IGDFQNGKRV SLSVYLGEFF DIHLFVNGTV TQGDQRVSM PYASKGLYLE TEAGYYKLSG EAYGFVARID GSGNFQVLLS DRYFNKTCGL CGNFNIFAED DFMTQEGTLT S DPYDFANS ...String:
AEGTRGRSST ARCSLFGSDF VNTFDGSMYS FAGYCSYLLA GGCQKRSFSI IGDFQNGKRV SLSVYLGEFF DIHLFVNGTV TQGDQRVSM PYASKGLYLE TEAGYYKLSG EAYGFVARID GSGNFQVLLS DRYFNKTCGL CGNFNIFAED DFMTQEGTLT S DPYDFANS WALSSGEQWC ERASPPSSSC NISSGEMQKG LWEQCQLLKS TSVFARCHPL VDPEPFVALC EKTLCECAGG LE CACPALL EYARTCAQEG MVLYGWTDHS ACSPVCPAGM EYRQCVSPCA RTCQSLHINE MCQERCVDGC SCPEGQLLDE GLC VESTEC PCVHSGKRYP PGTSLSRDCN TCICRNSQWI CSNEECPGEC LVTGQSHFKS FDNRYFTFSG ICQYLLARDC QDHS FSIVI ETVQCADDRD AVCTRSVTVR LPGLHNSLVK LKHGAGVAMD GQDVQLPLLK GDLRIQHTVT ASVRLSYGED LQMDW DGRG RLLVKLSPVY AGKTCGLCGN YNGNQGDDFL TPSGLAEPRV EDFGNAWKLH GDCQDLQKQH SDPCALNPRM TRFSEE ACA VLTSPTFEAC HRAVSPLPYL RNCRYDVCSC SDGRECLCGA LASYAAACAG RGVRVAWREP GRCELNCPKG QVYLQCG TP CNLTCRSLSY PDEECNEACL EGCFCPPGLY MDERGDCVPK AQCPCYYDGE IFQPEDIFSD HHTMCYCEDG FMHCTMSG V PGSLLPDAVL SSPLSHRSKR

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Macromolecule #2: von Willebrand factor

MacromoleculeName: von Willebrand factor / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.208891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SLSCRPPMVK LVCPADNLRA EGLECTKTCQ NYDLECMSMG CVSGCLCPPG MVRHENRCVA LERCPCFHQG KEYAPGETVK IGCNTCVCQ DRKWNCTDHV CDATCSTIGM AHYLTFDGLK YLFPGECQYV LVQDYCGSNP GTFRILVGNK GCSHPSVKCK K RVTILVEG ...String:
SLSCRPPMVK LVCPADNLRA EGLECTKTCQ NYDLECMSMG CVSGCLCPPG MVRHENRCVA LERCPCFHQG KEYAPGETVK IGCNTCVCQ DRKWNCTDHV CDATCSTIGM AHYLTFDGLK YLFPGECQYV LVQDYCGSNP GTFRILVGNK GCSHPSVKCK K RVTILVEG GEIELFDGEV NVKRPMKDET HFEVVESGRY IILLLGKALS VVWDRHLSIS VVLKQTYQEK VCGLCGNFDG IQ NNDLTSS NLQVEEDPVD FGNSWKVSSQ CADTRKVPLD SSPATCHNNI MKQTMVDSSC RILTSDVFQD CNKLVDPEPY LDV CIYDTC SCESIGDCAC FCDTIAAYAH VCAQHGKVVT WRTATLCPQS CEERNLMENG YECMWRYNSC APACQVTCQH PEPL ACPVQ CVEGCHAHCP PGKILDELLQ TCVDPEDCPV CEVAGRRFAS GKKVTLNPSD PEHCQICHCD VVNLTCEACQ EPGGL VVPP HHHHHH

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 20 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 466373

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