[English] 日本語
Yorodumi
- PDB-7bee: Crystal structure of a Hsp47-collagen peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bee
TitleCrystal structure of a Hsp47-collagen peptide complex
Components
  • 21er collagen model peptide
  • Collagen-binding protein
KeywordsCHAPERONE / hsp / hsp47 / collagen
Function / homology
Function and homology information


Collagen biosynthesis and modifying enzymes / negative regulation of endopeptidase activity / collagen fibril organization / collagen binding / serine-type endopeptidase inhibitor activity / endoplasmic reticulum / extracellular space
Similarity search - Function
Serpin H1 / Serpin H1, serpin domain / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Collagen-binding protein
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.939 Å
AuthorsAbraham, E.T. / Gebauer, J.M. / Baumann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)73111208 Germany
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Collagen's primary structure determines collagen:HSP47 complex stoichiometry.
Authors: Abraham, E.T. / Oecal, S. / Morgelin, M. / Schmid, P.W.N. / Buchner, J. / Baumann, U. / Gebauer, J.M.
History
DepositionDec 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Collagen-binding protein
B: Collagen-binding protein
C: 21er collagen model peptide
D: 21er collagen model peptide
E: 21er collagen model peptide
F: 21er collagen model peptide
G: 21er collagen model peptide
H: 21er collagen model peptide


Theoretical massNumber of molelcules
Total (without water)100,0468
Polymers100,0468
Non-polymers00
Water6,215345
1
A: Collagen-binding protein
C: 21er collagen model peptide
D: 21er collagen model peptide
E: 21er collagen model peptide


Theoretical massNumber of molelcules
Total (without water)50,0234
Polymers50,0234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-39 kcal/mol
Surface area19040 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-77 kcal/mol
Surface area35150 Å2
MethodPISA
3
B: Collagen-binding protein
F: 21er collagen model peptide
G: 21er collagen model peptide
H: 21er collagen model peptide


Theoretical massNumber of molelcules
Total (without water)50,0234
Polymers50,0234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-37 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.683, 96.683, 187.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 35 through 367 or resid 375 through 412))
21(chain B and resid 35 through 412)
12(chain C and resid 0 through 18)
22(chain D and resid 0 through 18)
32(chain E and resid 0 through 18)
42(chain F and resid 0 through 18)
52(chain G and resid 0 through 18)
62(chain H and resid 0 through 18)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASPASP(chain A and (resid 35 through 367 or resid 375 through 412))AA35 - 3671 - 333
121GLUGLUASPASP(chain A and (resid 35 through 367 or resid 375 through 412))AA375 - 412341 - 378
211METMETASPASP(chain B and resid 35 through 412)BB35 - 4121 - 378
112ACEACEGLYGLY(chain C and resid 0 through 18)CC0 - 181 - 19
212ACEACEGLYGLY(chain D and resid 0 through 18)DD0 - 181 - 19
312ACEACEGLYGLY(chain E and resid 0 through 18)EE0 - 181 - 19
412ACEACEGLYGLY(chain F and resid 0 through 18)FF0 - 181 - 19
512ACEACEGLYGLY(chain G and resid 0 through 18)GG0 - 181 - 19
612ACEACEGLYGLYchain HHH0 - 181 - 19

NCS ensembles :
ID
1
2

-
Components

#1: Protein Collagen-binding protein / Serpin H1


Mass: 44283.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SERPINH1 / Production host: Escherichia coli (E. coli) / References: UniProt: E2RHY7
#2: Protein/peptide
21er collagen model peptide


Mass: 1913.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, 18-26% PEG 3350, 1-6% Tacsimate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.939→46.81 Å / Num. obs: 75968 / % possible obs: 99.75 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.17
Reflection shellResolution: 1.939→2.009 Å / Rmerge(I) obs: 0.8625 / Num. unique obs: 7346 / CC1/2: 0.674

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.13rc2_2986refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AU2

4au2


Resolution: 1.939→46.81 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 3838 5.07 %
Rwork0.2069 71857 -
obs0.2087 75695 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.06 Å2 / Biso mean: 47.8422 Å2 / Biso min: 25.52 Å2
Refinement stepCycle: final / Resolution: 1.939→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6687 0 0 345 7032
Biso mean---47.34 -
Num. residues----873
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3455X-RAY DIFFRACTION8.906TORSIONAL
12B3455X-RAY DIFFRACTION8.906TORSIONAL
21C523X-RAY DIFFRACTION8.906TORSIONAL
22D523X-RAY DIFFRACTION8.906TORSIONAL
23E523X-RAY DIFFRACTION8.906TORSIONAL
24F523X-RAY DIFFRACTION8.906TORSIONAL
25G523X-RAY DIFFRACTION8.906TORSIONAL
26H523X-RAY DIFFRACTION8.906TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9393-1.96390.33831730.3013243595
1.9639-1.98970.34011350.2872643100
1.9897-2.0170.32181400.28282648100
2.017-2.04580.28021210.26662658100
2.0458-2.07630.30641300.25462599100
2.0763-2.10880.28571350.25622673100
2.1088-2.14330.30111480.24952616100
2.1433-2.18030.29161510.24482620100
2.1803-2.21990.24241480.24332634100
2.2199-2.26260.30061180.24362707100
2.2626-2.30880.29741390.23152619100
2.3088-2.3590.24421470.23782661100
2.359-2.41390.25531690.23622625100
2.4139-2.47430.30031690.25422593100
2.4743-2.54120.29821170.24742711100
2.5412-2.61590.30941470.23862646100
2.6159-2.70040.27921600.24482625100
2.7004-2.79690.25831240.23392654100
2.7969-2.90880.27021300.23042696100
2.9088-3.04120.29331480.24122646100
3.0412-3.20150.25641230.23342718100
3.2015-3.4020.21891170.20822691100
3.402-3.66460.23391620.19922675100
3.6646-4.03320.22371300.18242722100
4.0332-4.61640.18321630.15732696100
4.6164-5.81440.20771480.16972755100
5.8144-46.810.2011460.1722891100

+
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://pdbjlvh1.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