[English] 日本語
Yorodumi
- EMDB-41401: Structural architecture of the acidic region of the B domain of c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41401
TitleStructural architecture of the acidic region of the B domain of coagulation factor V
Map dataPlasma Factor V - A1 domain local refinement map
Sample
  • Tissue: Coagulation plasma Factor V
    • Protein or peptide: Coagulation Plasma Factor V
KeywordsCoagulation / Pro-cofactor / Factor V / B Domain / Acidic Region / BLOOD CLOTTING
Function / homology
Function and homology information


response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation ...response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / blood coagulation / Platelet degranulation / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal ...Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Coagulation factor V
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsMohammed BM / Basore K / Summers B / Pelc LA / Di Cera E
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL049413, HL139554 and HL147821 United States
Childrens Discovery Institute of Washington University and St. Louis Childrens HospitalCDI-CORE-2015-505 and CDI-CORE-2019-813 United States
Foundation for Barnes-Jewish Hospital3770 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK020579 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA091842 United States
CitationJournal: J Thromb Haemost / Year: 2024
Title: Structural architecture of the acidic region of the B domain of coagulation factor V.
Authors: Bassem M Mohammed / Katherine Basore / Brock Summers / Leslie A Pelc / Enrico Di Cera /
Abstract: BACKGROUND: Coagulation factor (F)V features an A1-A2-B-A3-C1-C2 domain organization and functions as the inactive precursor of FVa, a component of the prothrombinase complex required for rapid ...BACKGROUND: Coagulation factor (F)V features an A1-A2-B-A3-C1-C2 domain organization and functions as the inactive precursor of FVa, a component of the prothrombinase complex required for rapid thrombin generation in the penultimate step of the coagulation cascade. An intramolecular interaction within the large B domain (residues 710-1545) involves the basic region (BR, residues 963-1008) and acidic region (AR, residues 1493-1537) and locks FV in its inactive state. However, structural information on this important regulatory interaction or on the separate architecture of the AR and BR remains elusive due to conformational disorder of the B domain.
OBJECTIVES: To reveal the structure of the BR-AR interaction or of its separate components.
METHODS: The structure of FV is solved by cryogenic electron microscopy.
RESULTS: A new 3.05 Å resolution cryogenic electron microscopy structure of FV confirms the overall organization of the A and C domains but resolves the segment 1507 to 1545 within a largely ...RESULTS: A new 3.05 Å resolution cryogenic electron microscopy structure of FV confirms the overall organization of the A and C domains but resolves the segment 1507 to 1545 within a largely disordered B domain. The segment contains most of the AR and is organized as recently reported in FV short, a spliced variant of FV with a significantly shorter and less disordered B domain.
CONCLUSION: The similar architecture of the AR in FV and FV short provides structural context for physiologically important interactions of this region with the BR in FV and with the basic C-terminal ...CONCLUSION: The similar architecture of the AR in FV and FV short provides structural context for physiologically important interactions of this region with the BR in FV and with the basic C-terminal end of tissue factor pathway inhibitor α in FV short.
History
DepositionJul 31, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41401.png

Downloads & links

-
Map

FileDownload / File: emd_41401.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasma Factor V - A1 domain local refinement map
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0504
Minimum - Maximum-0.5278997 - 0.90354216
Average (Standard dev.)0.00069886335 (±0.016954971)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_41401_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41401_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41401_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Coagulation plasma Factor V

EntireName: Coagulation plasma Factor V
Components
  • Tissue: Coagulation plasma Factor V
    • Protein or peptide: Coagulation Plasma Factor V

-
Supramolecule #1: Coagulation plasma Factor V

SupramoleculeName: Coagulation plasma Factor V / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Tissue: Blood

-
Macromolecule #1: Coagulation Plasma Factor V

MacromoleculeName: Coagulation Plasma Factor V / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Blood
SequenceString: AQLRQFYVAA QGISWSYRPE PTNSSLNLSV TSFKKIVYRE YEPYFKKEKP QSTISGLLGP TLYAEVGDII KVHFKNKADK PLSIHPQGIR YSKLSEGASY LDHTFPAEKM DDAVAPGREY TYEWSISEDS GPTHDDPPCL THIYYSHENL IEDFNSGLIG PLLICKKGTL ...String:
AQLRQFYVAA QGISWSYRPE PTNSSLNLSV TSFKKIVYRE YEPYFKKEKP QSTISGLLGP TLYAEVGDII KVHFKNKADK PLSIHPQGIR YSKLSEGASY LDHTFPAEKM DDAVAPGREY TYEWSISEDS GPTHDDPPCL THIYYSHENL IEDFNSGLIG PLLICKKGTL TEGGTQKTFD KQIVLLFAVF DESKSWSQSS SLMYTVNGYV NGTMPDITVC AHDHISWHLL GMSSGPELFS IHFNGQVLEQ NHHKVSAITL VSATSTTANM TVGPEGKWII SSLTPKHLQA GMQAYIDIKN CPKKTRNLKK ITREQRRHMK RWEYFIAAEE VIWDYAPVIP ANMDKKYRSQ HLDNFSNQIG KHYKKVMYTQ YEDESFTKHT VNPNMKEDGI LGPIIRAQVR DTLKIVFKNM ASRPYSIYPH GVTFSPYEDE VNSSFTSGRN NTMIRAVQPG ETYTYKWNIL EFDEPTENDA QCLTRPYYSD VDIMRDIASG LIGLLLICKS RSLDRRGIQR AADIEQQAVF AVFDENKSWY LEDNINKFCE NPDEVKRDDP KFYESNIMST INGYVPESIT TLGFCFDDTV QWHFCSVGTQ NEILTIHFTG HSFIYGKRHE DTLTLFPMRG ESVTVTMDNV GTWMLTSMNS SPRSKKLRLK FRDVKCIPDD DEDSYEIFEP PESTVMATRK MHDRLEPEDE ESDADYDYQN RLAAALGIRS FRNSSLNQEE EEFNLTALAL ENGTEFVSSN TDIIVGSNYS SPSNISKFTV NNLAEPQKAP SHQQATTAGS PLRHLIGKNS VLNSSTAEHS SPYSEDPIED PLQPDVTGIR LLSLGAGEFR SQEHAKRKGP KVERDQAAKH RFSWMKLLAH KVGRHLSQDT GSPSGMRPWE DLPSQDTGSP SRMRPWEDPP SDLLLLKQSN SSKILVGRWH LASEKGSYEI IQDTDEDTAV NNWLISPQNA SRAWGESTPL ANKPGKQSGH PKFPRVRHKS LQVRQDGGKS RLKKSQFLIK TRKKKKEKHT HHAPLSPRTF HPLRSEAYNT FSERRLKHSL VLHKSNETSL PTDLNQTLPS MDFGWIASLP DHNQNSSNDT GQASCPPGLY QTVPPEEHYQ TFPIQDPDQM HSTSDPSHRS SSPELSEMLE YDRSHKSFPT DISQMSPSSE HEVWQTVISP DLSQVTLSPE LSQTNLSPDL SHTTLSPELI QRNLSPALGQ MPISPDLSHT TLSPDLSHTT LSLDLSQTNL SPELSQTNLS PALGQMPLSP DLSHTTLSLD FSQTNLSPEL SHMTLSPELS QTNLSPALGQ MPISPDLSHT TLSLDFSQTN LSPELSQTNL SPALGQMPLS PDPSHTTLSL DLSQTNLSPE LSQTNLSPDL SEMPLFADLS QIPLTPDLDQ MTLSPDLGET DLSPNFGQMS LSPDLSQVTL SPDISDTTLL PDLSQISPPP DLDQIFYPSE SSQSLLLQEF NESFPYPDLG QMPSPSSPTL NDTFLSKEFN PLVIVGLSKD GTDYIEIIPK EEVQSSEDDY AEIDYVPYDD PYKTDVRTNI NSSRDPDNIA AWYLRSNNGN RRNYYIAAEE ISWDYSEFVQ RETDIEDSDD IPEDTTYKKV VFRKYLDSTF TKRDPRGEYE EHLGILGPII RAEVDDVIQV RFKNLASRPY SLHAHGLSYE KSSEGKTYED DSPEWFKEDN AVQPNSSYTY VWHATERSGP ESPGSACRAW AYYSAVNPEK DIHSGLIGPL LICQKGILHK DSNMPVDMRE FVLLFMTFDE KKSWYYEKKS RSSWRLTSSE MKKSHEFHAI NGMIYSLPGL KMYEQEWVRL HLLNIGGSQD IHVVHFHGQT LLENGNKQHQ LGVWPLLPGS FKTLEMKASK PGWWLLNTEV GENQRAGMQT PFLIMDRDCR MPMGLSTGII SDSQIKASEF LGYWEPRLAR LNNGGSYNAW SVEKLAAEFA SKPWIQVDMQ KEVIITGIQT QGAKHYLKSC YTTEFYVAYS SNQINWQIFK GNSTRNVMYF NGNSDASTIK ENQFDPPIVA RYIRISPTRA YNRPTLRLEL QGCEVNGCST PLGMENGKIE NKQITASSFK KSWWGDYWEP FRARLNAQGR VNAWQAKANN NKQWLEIDLL KIKKITAIIT QGCKSLSSEM YVKSYTIHYS EQGVEWKPYR LKSSMVDKIF EGNTNTKGHV KNFFNPPIIS RFIRVIPKTW NQSITLRLEL FGCDIY

UniProtKB: Coagulation factor V

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 2 / Number real images: 8429 / Average exposure time: 1.65 sec. / Average electron dose: 66.0 e/Å2
Details: 2 Grids imaged one at 0.1 mg/mL and the second at 0.2 mg/mL using the same acquisition parameters.

-
Image processing

Particle selectionNumber selected: 1257129
Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 680564
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

+
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