[English] 日本語
Yorodumi
- PDB-6c1r: Crystal structure of human C5a receptor in complex with an orthos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c1r
TitleCrystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist avacopan
Components
  • PMX53
  • Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera
KeywordsMEMBRANE PROTEIN/INHIBITOR / GPCR / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


complement component C5a signaling pathway / presynapse organization / complement component C5a receptor activity / response to peptidoglycan / sensory perception of chemical stimulus / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production ...complement component C5a signaling pathway / presynapse organization / complement component C5a receptor activity / response to peptidoglycan / sensory perception of chemical stimulus / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / cellular defense response / neutrophil chemotaxis / astrocyte activation / secretory granule membrane / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of epithelial cell proliferation / mRNA transcription by RNA polymerase II / microglial cell activation / electron transport chain / G protein-coupled receptor activity / cognition / positive regulation of angiogenesis / chemotaxis / apical part of cell / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / immune response / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / signal transduction / plasma membrane
Similarity search - Function
Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
PMX53 / avacopan / MALONATE ION / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TRIETHYLENE GLYCOL / Soluble cytochrome b562 / C5a anaphylatoxin chemotactic receptor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLiu, H. / Wang, L. / Wei, Z. / Zhang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Orthosteric and allosteric action of the C5a receptor antagonists.
Authors: Liu, H. / Kim, H.R. / Deepak, R.N.V.K. / Wang, L. / Chung, K.Y. / Fan, H. / Wei, Z. / Zhang, C.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 5, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera
L: PMX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,20613
Polymers48,4052
Non-polymers2,80211
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-9 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.411, 52.608, 83.865
Angle α, β, γ (deg.)90.000, 106.080, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules BL

#1: Protein Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera / Cytochrome b-562 / C5a anaphylatoxin chemotactic receptor / C5aR


Mass: 47505.480 Da / Num. of mol.: 1
Fragment: cytochrome (UNP residues 23-127) + C5a receptor (UNP residues 30-331)
Mutation: M29W, H124I, R128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, C5AR1, C5AR, C5R1 / Plasmid: pFastbac / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: P21730
#2: Protein/peptide PMX53


Type: Cyclic peptide / Mass: 899.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PMX53

-
Non-polymers , 7 types, 56 molecules

#3: Chemical ChemComp-EFD / avacopan / (2R,3S)-2-[4-(cyclopentylamino)phenyl]-1-(2-fluoro-6-methylbenzene-1-carbonyl)-N-[4-methyl-3-(trifluoromethyl)phenyl]piperidine-3-carboxamide


Mass: 581.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35F4N3O2
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 283 K / Method: lipidic cubic phase / pH: 6.5
Details: 25-32% PEG300, 100 mM MES, pH6.5, 90-120 mM sodium malonate, 1% P400, 5 uM avacopan, 5 uM PMX53

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2017
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 25865 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.052 / Rrim(I) all: 0.138 / Χ2: 0.946 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.244.10.99812110.4550.5221.1330.65994.8
2.24-2.284.90.94512790.5180.4561.0550.65197.9
2.28-2.325.30.87312600.7250.3960.9630.6498.7
2.32-2.375.90.80612800.7440.3490.8820.65899.2
2.37-2.426.20.6813170.860.2880.7410.6399.7
2.42-2.486.60.62112430.8570.2540.6730.67199.6
2.48-2.546.90.57113020.8960.2290.6170.672100
2.54-2.616.80.45312980.9180.1830.4890.725100
2.61-2.687.40.37912870.9470.1470.4070.721100
2.68-2.777.30.31813190.9550.1240.3420.735100
2.77-2.877.50.2812730.9640.1070.3010.782100
2.87-2.997.40.23613050.9740.0910.2540.854100
2.99-3.127.50.20213140.9820.0780.2170.9599.9
3.12-3.297.40.16812860.9830.0660.1811.11799.9
3.29-3.497.30.13413000.9890.0520.1441.28699.9
3.49-3.767.20.11313080.9930.0450.1221.664100
3.76-4.147.40.0913020.9940.0360.0971.2799.8
4.14-4.736.20.07412950.9950.0320.0811.39498.6
4.73-5.967.30.07313240.9950.0290.0791.17799.8
5.96-306.90.06713620.9950.0280.0731.18299.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZUD

4zud


Resolution: 2.2→27.359 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.2235 1264 5.06 %
Rwork0.1923 --
obs0.1939 24988 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.8 Å2 / Biso mean: 50.596 Å2 / Biso min: 20.57 Å2
Refinement stepCycle: final / Resolution: 2.2→27.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 196 45 3087
Biso mean--59.8 40.09 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053102
X-RAY DIFFRACTIONf_angle_d1.0064200
X-RAY DIFFRACTIONf_chiral_restr0.028500
X-RAY DIFFRACTIONf_plane_restr0.004499
X-RAY DIFFRACTIONf_dihedral_angle_d16.9691104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.28810.28961430.26232561270498
2.2881-2.39220.27471320.2342617274999
2.3922-2.51820.23321450.212326182763100
2.5182-2.67580.21821420.186926172759100
2.6758-2.88220.22341340.179626542788100
2.8822-3.17190.22391430.182726162759100
3.1719-3.630.23481390.190526712810100
3.63-4.56990.21981430.175826452788100
4.5699-27.36130.20481430.196927252868100
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)
13.12770.22680.94869.92517.30786.3671-0.2125-0.2045-0.08450.0837-0.38050.90260.1342-0.64770.67120.2155-0.0325-0.02440.34740.04090.4346-14.36643.6881-37.2846
24.16670.2231-4.06791.81430.24116.2736-0.34180.3763-0.463-0.1778-0.15110.33960.4013-0.67810.41880.2239-0.0272-0.05040.26220.00050.3268-7.4133-2.6149-42.297
33.83791.7358-4.20061.8088-1.70668.1873-0.13570.1197-0.0611-0.1520.03760.14290.2027-0.4560.04890.2402-0.0027-0.03310.22050.00990.3031-0.6147-0.3595-37.2673
49.8847-8.1057-2.1087.9615-2.3982.0046-0.26430.1909-0.9075-0.7611-0.36870.42281.87630.23760.510.7084-0.00510.06290.6283-0.00290.658113.047-2.2271-62.8976
51.437-1.0429-0.76323.62661.879.909-0.1725-0.1023-0.12660.2467-0.03640.29290.4797-0.09690.17770.1984-0.02290.00040.16190.02690.27233.3137-6.5401-33.5986
67.18913.5175-5.18573.434-2.66029.40540.1243-1.2552-0.57220.8491-0.4552-0.201-0.25980.7640.2490.4970.0303-0.00730.35580.06970.33593.91452.7249-20.2858
76.9298-0.31052.02755.4067-0.80482.1047-0.13060.9380.1906-0.7645-0.1927-0.05530.16050.11570.26690.3192-0.04880.02330.3441-0.00860.250910.098113.2462-53.2813
81.31580.35630.01671.80691.31145.9045-0.1231-0.05190.08880.0178-0.03360.2239-0.1685-0.12070.17790.19560.0481-0.01940.18730.03470.3328-2.298410.8855-35.0153
92.02460.2562-7.57283.1961.32479.50370.22351.0624-0.4686-0.4094-0.08260.4131-0.3321-0.4982-0.02930.50550.0241-0.17580.7121-0.01720.6522-11.10192.7421-59.698
107.05291.47963.69833.829-0.60623.0745-0.01361.0447-0.2053-1.14120.1771-0.187-0.3652-0.6067-0.11490.90720.01270.12961.0657-0.19390.4423-6.357917.7385-3.2386
112.00060.83575.58051.7833-0.25363.513-0.1844-1.31030.39690.3662-0.15710.5971-0.1205-1.8260.30770.7072-0.08560.19361.0935-0.26420.5194-9.718716.09846.99
122.01133.24917.38735.91371.25035.34970.1044-0.1261-0.61730.65650.1077-0.02350.5947-0.8169-0.24460.917-0.13230.14680.8016-0.28090.6033-6.19718.8653.3397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 65 )A30 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 97 )A66 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 139 )A98 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 149 )A140 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 180 )A150 - 180
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 211 )A181 - 211
7X-RAY DIFFRACTION7chain 'A' and (resid 212 through 237 )A212 - 237
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 305 )A238 - 305
9X-RAY DIFFRACTION9chain 'A' and (resid 306 through 327 )A306 - 327
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 68 )B12 - 68
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 90 )B69 - 90
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 110 )B91 - 110

+
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