[English] 日本語
Yorodumi
- EMDB-64088: The structure of FIPV RBD and cat APN complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64088
TitleThe structure of FIPV RBD and cat APN complex
Map data
Sample
  • Complex: The structure of FIPV RBD and cat APN complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsprotein / PROTEIN BINDING
Function / homology
Function and homology information


membrane alanyl aminopeptidase / alanyl aminopeptidase activity / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / cell differentiation / receptor-mediated virion attachment to host cell ...membrane alanyl aminopeptidase / alanyl aminopeptidase activity / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / cell differentiation / 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, Alphacoronavirus / 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 ...Spike glycoprotein, Alphacoronavirus / 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 / Aminopeptidase N-like , N-terminal domain superfamliy / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Aminopeptidase N
Similarity search - Component
Biological speciesFeline infectious peritonitis virus (strain 79-1146) / Felis catus (domestic cat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsSun JQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: To Be Published
Title: The structure of FIPV RBD and cat APN complex
Authors: Sun JQ
History
DepositionApr 9, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64088.png

Downloads & links

-
Map

FileDownload / File: emd_64088.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: 0.111
Minimum - Maximum-0.43334478 - 0.90824646
Average (Standard dev.)-0.00033267387 (±0.026850155)
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: #2

Fileemd_64088_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64088_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The structure of FIPV RBD and cat APN complex

EntireName: The structure of FIPV RBD and cat APN complex
Components
  • Complex: The structure of FIPV RBD and cat APN complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: The structure of FIPV RBD and cat APN complex

SupramoleculeName: The structure of FIPV RBD and cat APN complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Feline infectious peritonitis virus (strain 79-1146)

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Feline infectious peritonitis virus (strain 79-1146)
Molecular weightTheoretical: 19.159557 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TANLNNGFYP VASSEVGFVN KSVVLLPSFF TYTAVNITID LGMKLSGYGQ PIASTLSNIT LPMQDNNTDV YCIRSNQFSV YVHSTCKSS LWDNIFNQDC TDVLEATAVI KTGTCPFSFD KLNNYLTFNK FCLSLSPVGA NCKFDVAART RTNEQVVRSL Y VIYEEGDN IVGVPS

UniProtKB: Spike glycoprotein

-
Macromolecule #2: Aminopeptidase N

MacromoleculeName: Aminopeptidase N / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: membrane alanyl aminopeptidase
Source (natural)Organism: Felis catus (domestic cat)
Molecular weightTheoretical: 105.928375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EKNRSTESST AASTAAPTGP TTTVATTLDQ SKPWNVYRLP KTLIPDSYNV TLRPYLTPNN KGLYVFTGTN IVRFTCKEST NIVIIHSKR LNYTSHQGHM VALSGVGGFH PQPVIVRTEL VELTEYLVVH LQEPLVAGRQ YEMNSEFQGE LADDLAGFYR S EYMENGVK ...String:
EKNRSTESST AASTAAPTGP TTTVATTLDQ SKPWNVYRLP KTLIPDSYNV TLRPYLTPNN KGLYVFTGTN IVRFTCKEST NIVIIHSKR LNYTSHQGHM VALSGVGGFH PQPVIVRTEL VELTEYLVVH LQEPLVAGRQ YEMNSEFQGE LADDLAGFYR S EYMENGVK KVLATTHMQA TEARKSFPCF DEPAMKATFN ITIIHPNNLV ALSNMLPRGP SVPFGEDPTW KVTEFETTPI MS TYLLAYI VSEFSYVETR APSGVLIRIW ARPSAINQGH GDYALKVTGP ILDFFSQHYD TPYPLNKSDQ IALPDFNAGA MEN WGLVTY RESALLYDRQ SSSSGNQERV VTVIAHELAH QWFGNLVTLE WWNDLWLNEG FASYVEYLGA DFAEPTWNLK DLMV LNDVY RVMAVDALAS SHPLSTPASE INTPAQISEV FDSISYSKGA SVLRMLSNFL TEDLFKMGIA SYLHTYKYGN TIYLN LWEH LQQVVDKQPT IKLPDTVSAI MDRWILQMGF PVITVDTQTG TISQQHFLLD PQSVVTRPSQ FNYLWIVPIS SVRSGS PQA HYWLPGVEKA QNDLFKTTAN DWVLLNLNVT GYYLVNYDNE NWKKIQTQLQ TDLSVIPVIN RAQVIHDAFN LASAQKV PV TLALNNTLFL IQETEYMPWQ AALSSLSYFK LMFDRSEVYG PMKRYLKKQV TPLFNHFERV TKNWTDHPQT LMDQYSEI N AVSTACSYGV PECEKLAATL FAQWKKNPQN NPIHPNLRST VYCNAIAQGG EEEWNFVWEQ FLKAELVNEA DKLRGALAC SNQVWILNRF LSYTLDPNLI RKQDVTSTLS SISSNVVGQT LVWDFVQSNW KKLFQDYGTG SFSFSNLIQA VTRRFSTEFE LQQLEQFKK NNMDTGFGSA TRALEQALEK TKANLKWVKE NKDVVLRWFT ENS

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: 4 / 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: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302929
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