[English] 日本語
Yorodumi
- PDB-9b1r: Functional implication of the homotrimeric multidomain vacuolar s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b1r
TitleFunctional implication of the homotrimeric multidomain vacuolar sorting receptor 1 from Arabidopsis thaliana
ComponentsVacuolar-sorting receptor 1
KeywordsPROTEIN TRANSPORT / VSR1 / Golgi / Transporter / Receptor / ER / EGF / PA / TRX
Function / homology
Function and homology information


amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole / trans-Golgi network / late endosome / protein transport / Golgi membrane / calcium ion binding ...amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole / trans-Golgi network / late endosome / protein transport / Golgi membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
PA domain superfamily / PA domain / PA domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / EGF-like domain signature 2.
Similarity search - Domain/homology
Vacuolar-sorting receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPark, H. / Youn, B. / Park, D.J. / Puthanveettil, S.V. / Kang, C.
Funding support United States, 3items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2023-67013-39629 United States
United States Department of Agriculture (USDA)2003-35318-13672 United States
National Science Foundation (NSF, United States)MCB-2043248 United States
CitationJournal: Sci Rep / Year: 2024
Title: Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 (VSR1) from Arabidopsis thaliana.
Authors: Park, H. / Youn, B. / Park, D.J. / Puthanveettil, S.V. / Kang, C.
History
DepositionMar 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vacuolar-sorting receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4832
Polymers62,0581
Non-polymers4241
Water0
1
A: Vacuolar-sorting receptor 1
hetero molecules

A: Vacuolar-sorting receptor 1
hetero molecules

A: Vacuolar-sorting receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,4486
Polymers186,1753
Non-polymers1,2733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10830 Å2
ΔGint-5 kcal/mol
Surface area58010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.543, 145.543, 145.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

-
Components

#1: Protein Vacuolar-sorting receptor 1 / AtVSR1 / BP80-like protein b / AtBP80b / Epidermal growth factor receptor-like protein 1 / AtELP / ...AtVSR1 / BP80-like protein b / AtBP80b / Epidermal growth factor receptor-like protein 1 / AtELP / AtELP1 / Spot 3 protein


Mass: 62058.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VSR1, BP80B, ELP, ELP1, At3g52850, F8J2.20 / Production host: Drosophila (fruit flies) / References: UniProt: P93026
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: PEG, Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.0108 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0108 Å / Relative weight: 1
ReflectionResolution: 3.5→36.39 Å / Num. obs: 24159 / % possible obs: 98.24 % / Redundancy: 4.5 % / Biso Wilson estimate: 67.05 Å2 / CC1/2: 0.997 / Net I/σ(I): 21.72
Reflection shellResolution: 3.5→3.625 Å / Num. unique obs: 1125 / CC1/2: 0.909

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→36.39 Å / SU ML: 0.3363 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.5872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 2402 9.94 %
Rwork0.1803 21757 -
obs0.1839 24159 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.74 Å2
Refinement stepCycle: LAST / Resolution: 3.5→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 28 0 3337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613411
X-RAY DIFFRACTIONf_angle_d0.87024619
X-RAY DIFFRACTIONf_chiral_restr0.0529511
X-RAY DIFFRACTIONf_plane_restr0.0077597
X-RAY DIFFRACTIONf_dihedral_angle_d6.6302468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.570.2731080.2464881X-RAY DIFFRACTION66.69
3.57-3.650.23331140.23421092X-RAY DIFFRACTION83.69
3.65-3.730.24951390.20011242X-RAY DIFFRACTION92.5
3.74-3.820.25941480.20361286X-RAY DIFFRACTION97.35
3.83-3.930.23731450.18851294X-RAY DIFFRACTION98.76
3.93-4.050.1981580.1721348X-RAY DIFFRACTION99.87
4.05-4.170.22461380.16871304X-RAY DIFFRACTION99.93
4.18-4.320.20651520.15761334X-RAY DIFFRACTION100
4.33-4.50.19931440.17221331X-RAY DIFFRACTION100
4.5-4.70.18951460.14691348X-RAY DIFFRACTION100
4.7-4.950.17751370.16921353X-RAY DIFFRACTION100
4.95-5.260.17891440.16551322X-RAY DIFFRACTION100
5.26-5.660.22661500.18451314X-RAY DIFFRACTION100
5.67-6.230.22931490.1851332X-RAY DIFFRACTION100
6.23-7.130.18971490.2051334X-RAY DIFFRACTION100
7.14-8.960.19551440.1741335X-RAY DIFFRACTION99.86
8.99-36.390.25311370.17711307X-RAY DIFFRACTION97.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.66530597909-0.5078613997740.08241043703062.616188967440.2214728684134.542294943070.3357516188510.6269997284730.059907630799-0.892645906018-0.5440503161720.065565617782-0.4941346227890.1763056758780.1757276723770.7065773667880.19698410449-0.04981623222520.658168865310.07359847930210.4255318091547.17478042577-26.3938590153-47.5101973577
21.75875386131-0.5619912236530.5641134899212.18708792214-0.9417186706111.81044210045-0.0079005138897-0.1058195832520.08380547978340.148129168871-0.0518695660459-0.0934597088813-0.2387691486060.02366542354680.04929278182730.356152824029-0.0635704579513-0.009326820271990.4390021566190.02930894056030.329658679306-16.171651924310.4050193748-23.8635456638
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 175 )21 - 1751 - 137
22chain 'A' and (resid 176 through 465 )176 - 465138 - 427

+
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