[English] 日本語
Yorodumi
- PDB-8tys: Adaptive mechanism of collagen IV scaffold assembly in Drosophila... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tys
TitleAdaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of tissue-extracted NC1 hexamer
Components
  • Collagen IV, chain Viking
  • Collagen alpha-1(IV) chain
KeywordsSTRUCTURAL PROTEIN / collagen IV / trimerization domain / hexamer assembly / basement membrane
Function / homology
Function and homology information


post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / collagen type IV trimer / Integrin cell surface interactions / dorsal closure / somatic muscle development ...post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / collagen type IV trimer / Integrin cell surface interactions / dorsal closure / somatic muscle development / extracellular matrix structural constituent conferring tensile strength / basement membrane organization / intestinal epithelial structure maintenance / cardiac muscle cell development / extracellular matrix structural constituent / basement membrane / extracellular matrix / : / extracellular space
Similarity search - Function
Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin fold
Similarity search - Domain/homology
Collagen alpha-1(IV) chain / Viking, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBoudko, S.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK018381 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK131101 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Collagen IV of basement membranes: IV. Adaptive mechanism of collagen IV scaffold assembly in Drosophila.
Authors: Summers, J.A. / Yarbrough, M. / Liu, M. / McDonald, W.H. / Hudson, B.G. / Pastor-Pareja, J.C. / Boudko, S.P.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 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: Collagen alpha-1(IV) chain
B: Collagen IV, chain Viking
C: Collagen alpha-1(IV) chain
D: Collagen alpha-1(IV) chain
E: Collagen IV, chain Viking
F: Collagen alpha-1(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,24012
Polymers153,0186
Non-polymers2226
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.209, 145.209, 106.491
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "D" and resid 5 through 227)
d_1ens_2(chain "B" and resid 3 through 227)
d_2ens_2chain "E"
d_1ens_3chain "C"
d_2ens_3(chain "F" and (resid 2 through 198 or (resid 199...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLYGLYASNASNAA5 - 2276 - 228
d_2ens_1GLYGLYASNASNDD5 - 2276 - 228
d_1ens_2SERSERARGARGBB3 - 2274 - 228
d_2ens_2SERSERARGARGEE3 - 2274 - 228
d_1ens_3TYRTYRASNASNCC2 - 2273 - 228
d_2ens_3TYRTYRASNASNFF2 - 2273 - 228

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.721686076597, -0.304772463807, -0.621516654766), (-0.320045954685, -0.649222459316, 0.689986076099), (-0.613791327518, 0.696867235293, 0.370993615362)-80.8431852723, -2.88529224146, -34.8501071895
2given(-0.722850887983, -0.299964798378, -0.622501175481), (-0.322354081261, -0.65045035405, 0.687751541773), (-0.61120736255, 0.697807607189, 0.373483739022)-81.0578707814, -2.8292199228, -34.9380689823
3given(-0.722089210415, -0.310374771352, -0.618267477319), (-0.317346111497, -0.645519359228, 0.694691444009), (-0.614718323885, 0.697833976079, 0.367626337617)-80.7864031948, -2.60701323775, -34.9971705604

-
Components

#1: Protein
Collagen alpha-1(IV) chain / Collagen IV / chain Cg25c


Mass: 25383.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P08120
#2: Protein Collagen IV, chain Viking


Mass: 25742.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VMV5
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 35% MPD, 0.1 M NaCl, 100mM HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.9→40.63 Å / Num. obs: 28410 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 76.53 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.039 / Rrim(I) all: 0.093 / Net I/σ(I): 17.3
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4562 / Rpim(I) all: 0.2 / Rrim(I) all: 0.49

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
pointlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→40.63 Å / SU ML: 0.4428 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2773 1335 4.7 %
Rwork0.2411 27053 -
obs0.2428 28388 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.82 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10466 0 6 0 10472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001710732
X-RAY DIFFRACTIONf_angle_d0.521314597
X-RAY DIFFRACTIONf_chiral_restr0.04331571
X-RAY DIFFRACTIONf_plane_restr0.00361920
X-RAY DIFFRACTIONf_dihedral_angle_d12.14233853
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.694285570663
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.843089991331
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.875467307331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.36141400.33952682X-RAY DIFFRACTION100
3-3.120.34681420.32192672X-RAY DIFFRACTION100
3.12-3.270.35071480.32182677X-RAY DIFFRACTION100
3.27-3.440.35571190.29262722X-RAY DIFFRACTION100
3.44-3.650.30411310.27932680X-RAY DIFFRACTION99.96
3.65-3.940.32731170.27122721X-RAY DIFFRACTION100
3.94-4.330.28781150.24452720X-RAY DIFFRACTION100
4.33-4.960.24081520.21452691X-RAY DIFFRACTION100
4.96-6.240.25791260.21452732X-RAY DIFFRACTION100
6.24-40.630.22861450.18782756X-RAY DIFFRACTION99.83

+
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