[English] 日本語
Yorodumi
- PDB-8typ: Complement Protease C1s Inhibited by 6-(4-phenylpiperazin-1-yl)py... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8typ
TitleComplement Protease C1s Inhibited by 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide
ComponentsComplement C1s subcomponent
KeywordsIMMUNE SYSTEM / complement / protease / inhibitor
Function / homology
Function and homology information


complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis ...complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / 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 / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-SQT / Complement C1s subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGeisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: J Immunol. / Year: 2024
Title: Inhibition of the C1s Protease and the Classical Complement Pathway by 6-(4-Phenylpiperazin-1-yl)Pyridine-3-Carboximidamide and Chemical Analogs.
Authors: Xu, X. / Herdendorf, T.J. / Duan, H. / Rohlik, D.L. / Roy, S. / Zhou, H. / Alkhateeb, H. / Khandelwal, S. / Zhou, Q. / Li, P. / Arepally, G.M. / Walker, J.K. / Garcia, B.L. / Geisbrecht, B.V.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement C1s subcomponent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0383
Polymers38,0241
Non-polymers1,0142
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.710, 79.818, 60.441
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Complement C1s subcomponent


Mass: 38023.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Plasmid: pCDNA3.1 / Cell line (production host): HEK293(t) / Production host: Homo sapiens (human) / References: UniProt: P09871
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SQT / 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide


Mass: 281.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate 0.1 M Tris-HCl (pH 8.1) PEG-4000 24% (w/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35443 / % possible obs: 97.1 % / Redundancy: 6.1 % / CC1/2: 0.973 / CC star: 0.993 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.065 / Rrim(I) all: 0.168 / Χ2: 1.013 / Net I/σ(I): 7.9 / Num. measured all: 214518
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.863.50.96529090.4640.7960.5371.1131.04980.6
1.86-1.944.50.76633830.6110.8710.3880.8641.02992.7
1.94-2.035.50.60135510.7450.9240.2780.6651.00698
2.03-2.135.90.45736400.840.9560.2050.5021.01499.6
2.13-2.276.30.3736170.9150.9780.1590.4030.993100
2.27-2.447.10.29836620.950.9870.120.3210.997100
2.44-2.6970.22436270.970.9920.0910.2421.014100
2.69-3.086.50.17136500.9760.9940.0730.1861.006100
3.08-3.886.90.12236720.9870.9970.050.1320.999100
3.88-506.80.09737320.9920.9980.040.1051.051100

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.03 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 2000 5.66 %
Rwork0.1854 --
obs0.1859 35339 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 70 335 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072524
X-RAY DIFFRACTIONf_angle_d0.9083427
X-RAY DIFFRACTIONf_dihedral_angle_d11.661937
X-RAY DIFFRACTIONf_chiral_restr0.057369
X-RAY DIFFRACTIONf_plane_restr0.007442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.3551050.2951756X-RAY DIFFRACTION72
1.84-1.890.30911320.26362180X-RAY DIFFRACTION87
1.89-1.950.22021370.24422307X-RAY DIFFRACTION95
1.95-2.010.21951450.22962395X-RAY DIFFRACTION97
2.01-2.080.22431470.19822454X-RAY DIFFRACTION99
2.08-2.170.18511450.19712435X-RAY DIFFRACTION100
2.17-2.270.19751480.18692463X-RAY DIFFRACTION100
2.27-2.390.19841460.18432441X-RAY DIFFRACTION100
2.39-2.530.19791490.18572471X-RAY DIFFRACTION100
2.53-2.730.21991490.19142473X-RAY DIFFRACTION100
2.73-30.18821480.1932484X-RAY DIFFRACTION100
3.01-3.440.1841480.18282475X-RAY DIFFRACTION100
3.44-4.330.16361490.15452481X-RAY DIFFRACTION100
4.33-48.030.18861520.16982524X-RAY DIFFRACTION100
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)
10.0087-0.06910.0545-0.08550.370.38560.02540.0676-0.0241-0.0451-0.0921-0.0824-0.1239-0.0321-0.00930.26-0.00190.02270.2094-0.02920.16910.616112.864238.7133
20.9129-0.13310.06041.54980.08951.7265-0.043-0.0495-0.00870.0424-0.01150.10160.0314-0.0697-00.1143-0.00330.0030.1463-0.00490.1489.67680.41147.1024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 357 through 433 )
2X-RAY DIFFRACTION2chain 'A' and (resid 434 through 683 )

+
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