[English] 日本語
Yorodumi
- EMDB-32622: Cryo-EM structure of VWF D'D3 dimer (R1136M/E1143M mutant) comple... -

+
Open data


ID or keywords:

Loading...

-
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 ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsblood / VWF / von Willebrand factor / von Willebrand disease / blood coagulation / blood clotting / multimer assembly / VWF assembly / D'D3 domain / D1D2 domain / D'D3 dimer / D1D2 Dimer / VWF Tube / repeating unit
Function / homology
Function and homology information


Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / 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 / protease binding / collagen-containing extracellular matrix / 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, 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 (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 signature. / 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32622.png

Downloads & links

-
Map

FileDownload / File: emd_32622.map.gz / Format: CCP4 / Size: 49.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 231 pix.
= 224.07 Å		0.97 Å/pix.
x 281 pix.
= 272.57 Å		0.97 Å/pix.
x 201 pix.
= 194.97 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Sample components

-
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 ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

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

-
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

UniProtKB: von Willebrand factor

-
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

UniProtKB: von Willebrand factor

-
Macromolecule #3: CALCIUM ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more