[English] 日本語
Yorodumi
- EMDB-39694: The structure of PDCoV RBD and dog APN complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39694
TitleThe structure of PDCoV RBD and dog APN complex
Map data
Sample
  • Complex: The PDCoV RBD-dAPN complex
    • Protein or peptide: Spike protein
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsPDCoV / PROTEIN BINDING / ISOMERASE
Function / homology
Function and homology information


membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell ...membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / proteolysis / extracellular space / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain ...Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike protein / Aminopeptidase N
Similarity search - Component
Biological speciesCanis lupus familiaris (dog) / Porcine deltacoronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsSun JQ / Niu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: To Be Published
Title: Cross-species recognition of two porcine coronaviruses to the aminopeptidase N in dogs and other species
Authors: Sun JQ
History
DepositionApr 7, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_39694.png

Downloads & links

-
Map

FileDownload / File: emd_39694.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 400 pix.
= 276. Å		0.69 Å/pix.
x 400 pix.
= 276. Å		0.69 Å/pix.
x 400 pix.
= 276. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.141
Minimum - Maximum-0.20763646 - 0.6782167
Average (Standard dev.)0.0025932929 (±0.029195989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_39694_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39694_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The PDCoV RBD-dAPN complex

EntireName: The PDCoV RBD-dAPN complex
Components
  • Complex: The PDCoV RBD-dAPN complex
    • Protein or peptide: Spike protein
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

-
Supramolecule #1: The PDCoV RBD-dAPN complex

SupramoleculeName: The PDCoV RBD-dAPN complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Canis lupus familiaris (dog)

-
Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porcine deltacoronavirus
Molecular weightTheoretical: 14.652571 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VTLPKLPELE VVQLNISAHM DFGEARLDSV TINGNTSYCV TKPYFRLETN FMCTGCTMNL RTDTCSFDLS AVNNGMSFSQ FCLSTESGA CEMKIIVTYV WNYLLRQRLY VTAVEGQTHT GTTSVHATDT SSV

UniProtKB: Spike protein

-
Macromolecule #2: Aminopeptidase N

MacromoleculeName: Aminopeptidase N / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: membrane alanyl aminopeptidase
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 106.801773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EKNKNAESSP VSSPVSSPVS SPVSPTNPST TAATTLAQSK PWNHYRLPKT LIPSSYNVTL RPYLTPNSNG LYTFKGSSTV RFTCKESTS MIIIHSKKLN YTNIQGQRVA LRGVGGSQAP AIDRTELVEV TEYLVVHLRE PLQVNSQYEM DSKFEGELAD D LAGFYRSE ...String:
EKNKNAESSP VSSPVSSPVS SPVSPTNPST TAATTLAQSK PWNHYRLPKT LIPSSYNVTL RPYLTPNSNG LYTFKGSSTV RFTCKESTS MIIIHSKKLN YTNIQGQRVA LRGVGGSQAP AIDRTELVEV TEYLVVHLRE PLQVNSQYEM DSKFEGELAD D LAGFYRSE YTENGVKKVL ATTQMQAADA RKSFPCFDEP AMKATFNITL IHPSNLVALS NMLPRGPSVP FTEEPNWNVT EF ETTPIMS TYLLAYIVSE FKNVQENTPS NVLIRIWARP SAMDQGHGNY ALRVTGPILD FFSRHYDTPY PLNKSDQIAL PDF NAGAME NWGLVTYRES ALLYDPQSSS IGNKERVVTV IAHELAHQWF GNLVTLEWWN DLWLNEGFAS YVEYLGADYA EPTW NLKDL IVLNEVYRVM AVDALASSHP LSSPASEVNT PAQISEVFDS ISYSKGASVL RMLSSFLTED LFKKGVASYL HTFAY QNTI YLDLWNHLQW ALGNQTAINL PYTVNAIMDR WILQMGFPVV TVDTTTGTLS QKHFLLDPQS NVTRPSKFNY LWIIPI SSV KSGTQQAHYW MPDNAKVQND LFKTTGDEWV LLNLNVTGYY LVNYDQNNWK KIHTQLQTDL SVIPVINRAQ VIHDTFD LA SAQIVPVTLA LNSTLFLNQE TEYMPWEAAL SSLSYFKLMF DRSEVYGPMK NYLRKQVTPL FNHFEKITQN WTDHPQTL T EQYNEINAVS TACTYGVPKC KDLVSTLFAE WRKNPQNNPI YPNLRSTVYC NAIAQGGEEE WNFVWEQFRN TSLVNEADK LRSALACSTQ VWILNRYLSY TLNPEFIRKQ DVISTLSSIA SNVIGQSLAW DFIQSNWKKL FEDYGTGSFS FSNLIQAVTR RFSTEFELQ QLEQFKANNM DTGFGSGTRA LEQALEKTKA NIKWVKENKE AVLQWFRENS Q

UniProtKB: Aminopeptidase N

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90772
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