[English] 日本語
Yorodumi
- PDB-4afu: Human Chymase - Fynomer Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4afu
TitleHuman Chymase - Fynomer Complex
Components
  • CHYMASE
  • FYNOMER
KeywordsHYDROLASE/DE NOVO PROTEIN / HYDROLASE-DE NOVO PROTEIN COMPLEX / INHIBITOR / SERINE PROTEASE
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity ...chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity / protein maturation / peptide binding / secretory granule / protein catabolic process / cellular response to glucose stimulus / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / : / endopeptidase activity / serine-type endopeptidase activity / extracellular space / extracellular region / cytosol
Similarity search - Function
SH3 Domains / SH3 type barrels. / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain ...SH3 Domains / SH3 type barrels. / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsSchlatter, D. / Brack, S. / Banner, D.W. / Batey, S. / Benz, J. / Bertschinger, J. / Huber, W. / Joseph, C. / Rufer, A. / Van Der Kloosters, A. ...Schlatter, D. / Brack, S. / Banner, D.W. / Batey, S. / Benz, J. / Bertschinger, J. / Huber, W. / Joseph, C. / Rufer, A. / Van Der Kloosters, A. / Weber, M. / Grabulovski, D. / Hennig, M.
CitationJournal: Mabs / Year: 2012
Title: Generation, Characterization and Structural Data of Chymase Binding Proteins Based on the Human Fyn Kinase SH3 Domain.
Authors: Schlatter, D. / Brack, S. / Banner, D.W. / Batey, S. / Benz, J. / Bertschinger, J. / Huber, W. / Joseph, C. / Rufer, A. / Van Der Klooster, A. / Weber, M. / Grabulovski, D. / Hennig, M.
History
DepositionJan 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references / Structure summary
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHYMASE
B: CHYMASE
C: FYNOMER
D: FYNOMER


Theoretical massNumber of molelcules
Total (without water)69,6034
Polymers69,6034
Non-polymers00
Water93752
1
A: CHYMASE
C: FYNOMER


Theoretical massNumber of molelcules
Total (without water)34,8022
Polymers34,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-3.3 kcal/mol
Surface area12440 Å2
MethodPISA
2
B: CHYMASE
D: FYNOMER


Theoretical massNumber of molelcules
Total (without water)34,8022
Polymers34,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-4.4 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.992, 59.057, 158.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CHYMASE / ALPHA-CHYMASE / MAST CELL PROTEASE I


Mass: 25066.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23946, chymase
#2: Protein FYNOMER


Mass: 9734.651 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAINS C, D: ARTIFICIAL PROTEIN BASED ON SH3 DOMAIN OF P06241 (83-145)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M SODIUM CHLORIDE, 0.1 M BIS-TRIS PH 6.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0.464
ReflectionResolution: 1.82→50 Å / Num. obs: 50464 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.13 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.72
Reflection shellResolution: 1.82→1.91 Å / Redundancy: 5.48 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.48 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE STRUCTURE

Resolution: 1.82→47.276 Å / σ(F): 0.02 / Phase error: 28.79 / Stereochemistry target values: TWIN_LSQ_F / Details: ALMOST PERFECT TWIN
RfactorNum. reflection% reflection
Rfree0.2252 2530 5.2 %
Rwork0.1881 --
obs0.1898 48335 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.59 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.2783 Å20 Å20 Å2
2--4.4324 Å20 Å2
3----6.7106 Å2
Refinement stepCycle: LAST / Resolution: 1.82→47.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 0 52 4409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064480
X-RAY DIFFRACTIONf_angle_d1.0046069
X-RAY DIFFRACTIONf_dihedral_angle_d16.5971613
X-RAY DIFFRACTIONf_chiral_restr0.066659
X-RAY DIFFRACTIONf_plane_restr0.005777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8202-1.85520.3791220.38332095X-RAY DIFFRACTION75
1.8552-1.89310.38671260.37632185X-RAY DIFFRACTION80
1.8931-1.93420.34361260.35512272X-RAY DIFFRACTION83
1.9342-1.97920.35451150.33172375X-RAY DIFFRACTION86
1.9792-2.02870.34761180.31892523X-RAY DIFFRACTION90
2.0287-2.08350.31321300.30312492X-RAY DIFFRACTION92
2.0835-2.14480.30081580.29742537X-RAY DIFFRACTION91
2.1448-2.2140.32811310.28442600X-RAY DIFFRACTION93
2.214-2.29310.33271470.29312581X-RAY DIFFRACTION93
2.2931-2.38490.30711460.28492627X-RAY DIFFRACTION94
2.3849-2.49340.28451440.28082613X-RAY DIFFRACTION94
2.4934-2.62480.29771370.26932643X-RAY DIFFRACTION95
2.6248-2.78910.26251510.25492660X-RAY DIFFRACTION94
2.7891-3.00430.24241460.22742655X-RAY DIFFRACTION95
3.0043-3.30620.19941250.18142711X-RAY DIFFRACTION95
3.3062-3.78370.19091370.13912680X-RAY DIFFRACTION95
3.7837-4.76370.14421450.09422725X-RAY DIFFRACTION95
4.7637-28.99920.17241530.11532877X-RAY DIFFRACTION95

+
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