[English] 日本語
Yorodumi
- PDB-1g96: HUMAN CYSTATIN C; DIMERIC FORM WITH 3D DOMAIN SWAPPING -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g96
TitleHUMAN CYSTATIN C; DIMERIC FORM WITH 3D DOMAIN SWAPPING
ComponentsCYSTATIN C
Keywordshydrolase inhibitor / human cystatin C dimer / 3D domain swapping / amyloid formation / inhibitor of C1 and C13 cysteine proteases / AMYLOID ANGIOPATHY AND CEREBRAL HEMORRHAGE
Function / homology
Function and homology information


negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization ...negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization / negative regulation of proteolysis / Post-translational protein phosphorylation / defense response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / tertiary granule lumen / amyloid-beta binding / protease binding / vesicle / ficolin-1-rich granule lumen / Amyloid fiber formation / endoplasmic reticulum lumen / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJanowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Grubb, A. / Abrahamson, M. / Jaskolski, M.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping.
Authors: Janowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Grubb, A. / Abrahamson, M. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression of selenomethionyl derivative and preliminary crystallographic studies of human cystatin C
Authors: Kozak, M. / Jankowska, E. / Janowski, R. / Grzonka, Z. / Grubb, A. / Alvarez Fernandez, M. / Abrahamson, M. / Jaskolski, M.
#2: Journal: Embo J. / Year: 1988
Title: The 2.0 angstrom X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteases
Authors: Bode, W. / Engh, R. / Musil, D. / Thiele, U. / Huber, R. / Karshikov, A. / Brzin, J. / Kos, J. / Turk, V.
#3: Journal: J.Mol.Biol. / Year: 1997
Title: NMR structural studies of human cystatin C dimers and monomers
Authors: Ekiel, I. / Abrahamson, M. / Fulton, D.B. / Lindahl, P. / Storer, A.C. / Levadoux, W. / Lafrance, M. / Labelle, S. / Pomerleau, Y. / Groleau, D. / LeSauter, L. / Gehring, K.
History
DepositionNov 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYSTATIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4933
Polymers13,3651
Non-polymers1282
Water39622
1
A: CYSTATIN C
hetero molecules

A: CYSTATIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9856
Polymers26,7302
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6420 Å2
ΔGint-38 kcal/mol
Surface area13750 Å2
MethodPISA
2
A: CYSTATIN C
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)107,94224
Polymers106,9218
Non-polymers1,02016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area40850 Å2
ΔGint-176 kcal/mol
Surface area39830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.53, 140.53, 140.53
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Cell settingcubic
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-301-

CL

DetailsHuman cystatin C in the present structure forms crystallographic dimers with 3D swapped domains. The dimer is generated by two-fold rotation of the 4(2) axis using the following transformation: 1/2-x, -y, z.

-
Components

#1: Protein CYSTATIN C / GAMMA-TRACE / POST-GAMMA-GLOBULIN


Mass: 13365.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHD 313 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P01034
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Lyophilized protein was dissolved in 100 mM sodium acetate buffer pH 4.8 containing 20 mM CaCl2. Droplets were equilibrated against 1 ml of reservoir with analogous buffer/CaCl2 solution. ...Details: Lyophilized protein was dissolved in 100 mM sodium acetate buffer pH 4.8 containing 20 mM CaCl2. Droplets were equilibrated against 1 ml of reservoir with analogous buffer/CaCl2 solution. After 2 and 4 days, the reservoir solution was supplemented with 100 microliters of MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mMsodium acetate1drop
320 mM1dropCaCl2
4MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2000
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 8429 / Num. obs: 8429 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.5 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 167936
Reflection shell
*PLUS
% possible obs: 93.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-terminally truncated chicken cystatin (1cew.pdb) converted to a polyalanine chain and limited to those fragments that had been modeled in electron density (residues 86-90 not included)

1cew


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: individual isotropic / Cross valid method: free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.249 815 9.6 %random
Rwork0.22 ---
all0.216 8500 --
obs0.216 8429 99.2 %-
Solvent computationSolvent model: flat model / Bsol: 38.73 Å2 / ksol: 0.33 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 7 22 900
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d1.85
X-RAY DIFFRACTIONc_mcbond_it2.411.5
X-RAY DIFFRACTIONc_mcangle_it4.032
X-RAY DIFFRACTIONc_scbond_it3.92
X-RAY DIFFRACTIONc_scangle_it6.082.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.331 70 8.3 %
Rwork0.328 714 -
obs-784 93.5 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.85

+
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