[English] 日本語
Yorodumi
- PDB-2o39: Human Adenovirus type 11 knob in complex with domains SCR1 and SC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o39
TitleHuman Adenovirus type 11 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, MCP)
Components
  • Fiber protein
  • Membrane cofactor protein
KeywordsVIRAL PROTEIN/immune system / Membrane cofactor protein / MCP / CD46 / Adenovirus / fiber knob / Ad11 / virus receptor complex / SCR / Short consensus repeat / CCP / complement control protein / VIRAL PROTEIN-immune system COMPLEX
Function / homology
Function and homology information


sequestering of extracellular ligand from receptor / inner acrosomal membrane / negative regulation of complement activation, classical pathway / T cell mediated immunity / positive regulation of transforming growth factor beta production / regulation of Notch signaling pathway / positive regulation of memory T cell differentiation / adhesion receptor-mediated virion attachment to host cell / positive regulation of regulatory T cell differentiation / positive regulation of interleukin-10 production ...sequestering of extracellular ligand from receptor / inner acrosomal membrane / negative regulation of complement activation, classical pathway / T cell mediated immunity / positive regulation of transforming growth factor beta production / regulation of Notch signaling pathway / positive regulation of memory T cell differentiation / adhesion receptor-mediated virion attachment to host cell / positive regulation of regulatory T cell differentiation / positive regulation of interleukin-10 production / single fertilization / complement activation, classical pathway / positive regulation of T cell proliferation / Regulation of Complement cascade / viral capsid / signaling receptor activity / virus receptor activity / adaptive immune response / cell adhesion / cadherin binding / symbiont entry into host cell / innate immune response / negative regulation of gene expression / focal adhesion / positive regulation of gene expression / host cell nucleus / cell surface / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Membrane cofactor protein CD46 / : / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily ...Membrane cofactor protein CD46 / : / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Membrane cofactor protein / Fiber protein
Similarity search - Component
Biological speciesHuman adenovirus 11p
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPersson, D.B. / Reiter, D.M. / Arnberg, N. / Stehle, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Adenovirus type 11 binding alters the conformation of its receptor CD46.
Authors: Persson, B.D. / Reiter, D.M. / Marttila, M. / Mei, Y.F. / Casasnovas, J.M. / Arnberg, N. / Stehle, T.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Membrane cofactor protein
D: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4229
Polymers73,1284
Non-polymers1,2935
Water61334
1
A: Fiber protein
C: Membrane cofactor protein
hetero molecules

A: Fiber protein
C: Membrane cofactor protein
hetero molecules

A: Fiber protein
C: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,57212
Polymers109,6926
Non-polymers1,8806
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
2
B: Fiber protein
D: Membrane cofactor protein
hetero molecules

B: Fiber protein
D: Membrane cofactor protein
hetero molecules

B: Fiber protein
D: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69215
Polymers109,6926
Non-polymers2,0009
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)106.140, 106.140, 68.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
DetailsTrimer consisting of three Ad11 chains and three CD46 SCR1 and SCR2 chains. The asymmetric unit contains two copies of an Ad11 chain, belonging to different trimers, and two copies of CD46, also belonging to different trimers. The biological units, the trimers, can be created through application of crystallographic symmetry operators.

-
Components

#1: Protein Fiber protein / pIV


Mass: 22046.545 Da / Num. of mol.: 2 / Fragment: residues 129-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 11p / Genus: Mastadenovirus / Species: Human adenovirus B / Strain: Slobiski / Gene: PIV / Plasmid: Pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 DE3 / References: UniProt: P35774
#2: Protein Membrane cofactor protein / Trophoblast leukocyte common antigen / TLX / CD46 antigen


Mass: 14517.551 Da / Num. of mol.: 2 / Fragment: SCR1 and SCR 2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD46, MCP / Plasmid: pBJ5 / Cell (production host): CHO cell / Cell line (production host): CHO-LEC3281 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P15529
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 35% PEG 200, 200mM CaCl2, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2006
RadiationMonochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→40 Å / Num. all: 20127 / Num. obs: 18738 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.23
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.64 / Num. unique all: 1710 / % possible all: 83

-
Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Adenovirus type 11 (unpublished) CD46 SCR1 and SCR2

Resolution: 2.85→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1869 -Random
Rwork0.238 ---
all0.238 20127 --
obs0.238 18738 93.1 %-
Refinement stepCycle: LAST / Resolution: 2.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 81 34 5249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBond angle1.5
X-RAY DIFFRACTIONBond length0.008

+
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