[English] 日本語
Yorodumi
- PDB-1elv: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEMENT C1S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1elv
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEMENT C1S PROTEASE
ComponentsCOMPLEMENT C1S COMPONENT
KeywordsHYDROLASE / TRYPSIN-LIKE SERIN PROTEASE / CCP (OR SUSHI OR SCR)MODULE
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 / innate immune response / serine-type endopeptidase activity / 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 / innate immune response / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / 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) ...Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Ribbon / Serine proteases, trypsin family, serine 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-NES / Complement C1s subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsGaboriaud, C. / Rossi, V. / Bally, I. / Arlaud, G. / Fontecilla-Camps, J.-C.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of the catalytic domain of human complement c1s: a serine protease with a handle.
Authors: Gaboriaud, C. / Rossi, V. / Bally, I. / Arlaud, G.J. / Fontecilla-Camps, J.C.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COMPLEMENT C1S COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6795
Polymers36,6871
Non-polymers9924
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.080, 79.650, 60.210
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein COMPLEMENT C1S COMPONENT


Mass: 36687.473 Da / Num. of mol.: 1
Fragment: CCP2-SP CATALYTIC FRAGMENT: ASP363-ASP-673 SEGMENT PRECEDED BY AN ASP-LEU SEQUENCE ADDED AT THE N-TERMINAL END
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: BAC-TO-BAC EXPRESSION SYSTEM / Plasmid: PNT-BAC/CCP2-AP-SP / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P09871, complement subcomponent C_overbar_1s_
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NES / 2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID


Mass: 229.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO6S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4K 34%, AMMONIUM SULFATE 100mM, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
250 mMTEA-HCl1drop
3145 mM1dropNaCl
434 %PEG40001reservoir
5100 mMammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. all: 39489 / Num. obs: 115710 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.037 / Net I/σ(I): 16.9
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.247 / % possible all: 75.8
Reflection
*PLUS
Num. obs: 39489 / Num. measured all: 115710 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 75.8 % / Rmerge(I) obs: 0.247

-
Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
WARPmodel building
REFMACrefinement
RefinementResolution: 1.7→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Lamzin (arp.dic)
Details: LIKELY BECAUSE OF RADIATION DAMAGES, THE INTERCHAIN DISULFIDE BRIDGE (A410-A534) IS NOT FORMED, SEVERAL CYSTEINES ARE OBSERVED WITH DUAL CONFORMATION (A371, A410, A580, A613) AND DENSITY IS ...Details: LIKELY BECAUSE OF RADIATION DAMAGES, THE INTERCHAIN DISULFIDE BRIDGE (A410-A534) IS NOT FORMED, SEVERAL CYSTEINES ARE OBSERVED WITH DUAL CONFORMATION (A371, A410, A580, A613) AND DENSITY IS LACKING AT THE END OF SEVERAL GLU (A351, A359, A372, A373, A385, A397, A402, A506), ASP (A357, A541), LYS (A629) AND MET (A545) RESIDUES. (THIS IS BRIEFLY DISCUSSED IN THE ABOVE REFERENCE).
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1969 5 %RANDOM
Rwork0.186 ---
all-38816 --
obs-38816 --
Displacement parametersBiso mean: 26.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 62 317 2712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.024
X-RAY DIFFRACTIONp_bond_d0.02
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_plane_restr0.016

+
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