[English] 日本語
Yorodumi
- PDB-6d48: Cell Surface Receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d48
TitleCell Surface Receptor
ComponentsMyeloid cell surface antigen CD33
KeywordsIMMUNE SYSTEM / Sialic Acid Binding / Transmembrane / Receptor / Siglec
Function / homology
Function and homology information


immune response-inhibiting signal transduction / positive regulation of protein tyrosine phosphatase activity / negative regulation of monocyte activation / sialic acid binding / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of calcium ion transport / negative regulation of tumor necrosis factor production / specific granule membrane ...immune response-inhibiting signal transduction / positive regulation of protein tyrosine phosphatase activity / negative regulation of monocyte activation / sialic acid binding / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of calcium ion transport / negative regulation of tumor necrosis factor production / specific granule membrane / positive regulation of protein secretion / cell-cell adhesion / peroxisome / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / signaling receptor activity / carbohydrate binding / protein phosphatase binding / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / Neutrophil degranulation / Golgi apparatus / cell surface / signal transduction / nucleoplasm / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myeloid cell surface antigen CD33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.776 Å
AuthorsHermans, S.J. / Miles, L.A. / Parker, M.W.
CitationJournal: Iscience / Year: 2019
Title: Small Molecule Binding to Alzheimer Risk Factor CD33 Promotes A beta Phagocytosis.
Authors: Miles, L.A. / Hermans, S.J. / Crespi, G.A.N. / Gooi, J.H. / Doughty, L. / Nero, T.L. / Markulic, J. / Ebneth, A. / Wroblowski, B. / Oehlrich, D. / Trabanco, A.A. / Rives, M.L. / Royaux, I. / ...Authors: Miles, L.A. / Hermans, S.J. / Crespi, G.A.N. / Gooi, J.H. / Doughty, L. / Nero, T.L. / Markulic, J. / Ebneth, A. / Wroblowski, B. / Oehlrich, D. / Trabanco, A.A. / Rives, M.L. / Royaux, I. / Hancock, N.C. / Parker, M.W.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Myeloid cell surface antigen CD33
F: Myeloid cell surface antigen CD33
G: Myeloid cell surface antigen CD33
H: Myeloid cell surface antigen CD33


Theoretical massNumber of molelcules
Total (without water)58,5934
Polymers58,5934
Non-polymers00
Water8,827490
1
E: Myeloid cell surface antigen CD33


Theoretical massNumber of molelcules
Total (without water)14,6481
Polymers14,6481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
F: Myeloid cell surface antigen CD33


Theoretical massNumber of molelcules
Total (without water)14,6481
Polymers14,6481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
G: Myeloid cell surface antigen CD33


Theoretical massNumber of molelcules
Total (without water)14,6481
Polymers14,6481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
H: Myeloid cell surface antigen CD33


Theoretical massNumber of molelcules
Total (without water)14,6481
Polymers14,6481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.801, 41.543, 107.498
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Myeloid cell surface antigen CD33 / Sialic acid-binding Ig-like lectin 3 / Siglec-3 / gp67


Mass: 14648.298 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20138
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.31 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 4000 100 mM Tris-HCl pH 8.5 10% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.776→42.48 Å / Num. obs: 51251 / % possible obs: 98.5 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.028 / Rrim(I) all: 0.052 / Net I/σ(I): 14.7
Reflection shellResolution: 1.776→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2673 / Rpim(I) all: 0.246 / Rrim(I) all: 0.464 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1496: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NKO

1nko


Resolution: 1.776→35.599 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 2485 4.85 %
Rwork0.1756 --
obs0.1774 51235 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.776→35.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 0 490 4530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014170
X-RAY DIFFRACTIONf_angle_d0.9795669
X-RAY DIFFRACTIONf_dihedral_angle_d12.7422503
X-RAY DIFFRACTIONf_chiral_restr0.062594
X-RAY DIFFRACTIONf_plane_restr0.008751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7761-1.81030.29061310.23052467X-RAY DIFFRACTION90
1.8103-1.84730.27681290.22072717X-RAY DIFFRACTION100
1.8473-1.88740.28641490.2062780X-RAY DIFFRACTION100
1.8874-1.93130.25261410.21772635X-RAY DIFFRACTION100
1.9313-1.97960.26181430.19612780X-RAY DIFFRACTION100
1.9796-2.03310.22481360.18612703X-RAY DIFFRACTION100
2.0331-2.0930.22071590.1682738X-RAY DIFFRACTION100
2.093-2.16050.22111180.1662723X-RAY DIFFRACTION100
2.1605-2.23770.19411330.17112735X-RAY DIFFRACTION100
2.2377-2.32730.20691380.17172726X-RAY DIFFRACTION100
2.3273-2.43320.21751340.17112773X-RAY DIFFRACTION100
2.4332-2.56140.22791560.1842694X-RAY DIFFRACTION99
2.5614-2.72190.2321360.18632736X-RAY DIFFRACTION100
2.7219-2.93190.20051280.17752745X-RAY DIFFRACTION99
2.9319-3.22680.22231620.18072722X-RAY DIFFRACTION99
3.2268-3.69330.20681400.16292687X-RAY DIFFRACTION98
3.6933-4.65160.16251310.14312728X-RAY DIFFRACTION97
4.6516-35.60610.2071210.18912661X-RAY DIFFRACTION92

+
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