[English] 日本語
Yorodumi
- PDB-5ao5: Endo180 D1-4, monoclinic form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ao5
TitleEndo180 D1-4, monoclinic form
ComponentsC-TYPE MANNOSE RECEPTOR 2
KeywordsENDOCYTOSIS / ENDOCYTIC RECEPTOR / FIBRONECTIN TYPE II DOMAIN / C-TYPE LECTIN DOMAIN / COLLAGEN / GELATIN
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / collagen catabolic process / collagen binding / endocytosis / osteoblast differentiation / signaling receptor activity / carbohydrate binding / focal adhesion / membrane
Similarity search - Function
Fibronectin, type II, collagen-binding / MRC2-like, N-terminal cysteine-rich domain / Seminal Fluid Protein PDC-109 (Domain B) / CD209-like, C-type lectin-like domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain ...Fibronectin, type II, collagen-binding / MRC2-like, N-terminal cysteine-rich domain / Seminal Fluid Protein PDC-109 (Domain B) / CD209-like, C-type lectin-like domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Kringle-like fold / Ribbon / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
C-type mannose receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsParacuellos, P. / Briggs, D.C. / Carafoli, F. / Loncar, T. / Hohenester, E.
CitationJournal: Structure / Year: 2015
Title: Insights Into Collagen Uptake by C-Type Mannose Receptors from the Crystal Structure of Endo180 Domains 1-4.
Authors: Paracuellos, P. / Briggs, D.C. / Carafoli, F. / Loncar, T. / Hohenester, E.
History
DepositionSep 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-TYPE MANNOSE RECEPTOR 2
B: C-TYPE MANNOSE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,66110
Polymers109,1852
Non-polymers4768
Water2,936163
1
A: C-TYPE MANNOSE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8315
Polymers54,5921
Non-polymers2384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-TYPE MANNOSE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8315
Polymers54,5921
Non-polymers2384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.370, 92.370, 127.650
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein C-TYPE MANNOSE RECEPTOR 2 / ENDO180 / C-TYPE LECTIN DOMAIN FAMILY 13 MEMBER E / ENDOCYTIC RECEPTOR 180 / MACROPHAGE MANNOSE ...ENDO180 / C-TYPE LECTIN DOMAIN FAMILY 13 MEMBER E / ENDOCYTIC RECEPTOR 180 / MACROPHAGE MANNOSE RECEPTOR 2 / UROKINASE-TYPE PLASMINOGEN ACTIVATOR RECEPTOR-ASSOCIATED PROTEIN / UPAR-ASSOCIATED PROTEIN / UROKINASE RECEPTOR-ASSOCIATED PROTEIN / CD280


Mass: 54592.484 Da / Num. of mol.: 2 / Fragment: DOMAINS 1-4, RESIDUES 35-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCEP-PU / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9UBG0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsVECTOR-DERIVED APLA AT N-TERMINUS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.48→62.8 Å / Num. obs: 50153 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 46.16 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TDQ, 3M7P, 1DQG

1tdq

3m7p

1dqg


Resolution: 2.48→60.158 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 2496 5 %
Rwork0.1936 --
obs0.1961 50150 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→60.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 24 163 7147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067221
X-RAY DIFFRACTIONf_angle_d0.9019746
X-RAY DIFFRACTIONf_dihedral_angle_d12.7332554
X-RAY DIFFRACTIONf_chiral_restr0.035983
X-RAY DIFFRACTIONf_plane_restr0.0031265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.52770.3141400.28222673X-RAY DIFFRACTION98
2.5277-2.57930.33431280.26432644X-RAY DIFFRACTION99
2.5793-2.63540.28971640.25162688X-RAY DIFFRACTION99
2.6354-2.69670.33731490.25982617X-RAY DIFFRACTION98
2.6967-2.76410.30951200.25352630X-RAY DIFFRACTION98
2.7641-2.83890.31171350.25192439X-RAY DIFFRACTION91
2.8389-2.92240.31181310.23772645X-RAY DIFFRACTION97
2.9224-3.01670.33171370.23152684X-RAY DIFFRACTION99
3.0167-3.12450.28781410.23092676X-RAY DIFFRACTION99
3.1245-3.24960.30171490.22292678X-RAY DIFFRACTION99
3.2496-3.39750.24131290.21982704X-RAY DIFFRACTION99
3.3975-3.57660.25431500.20282658X-RAY DIFFRACTION99
3.5766-3.80070.25711290.18262677X-RAY DIFFRACTION99
3.8007-4.09410.22241570.17352612X-RAY DIFFRACTION97
4.0941-4.5060.17411300.14242546X-RAY DIFFRACTION94
4.506-5.15770.18421420.14092717X-RAY DIFFRACTION99
5.1577-6.49690.19161380.17012706X-RAY DIFFRACTION99
6.4969-60.17560.24881270.18772660X-RAY DIFFRACTION95

+
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