[English] 日本語
Yorodumi
- PDB-4z9g: Crystal structure of human corticotropin-releasing factor recepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z9g
TitleCrystal structure of human corticotropin-releasing factor receptor 1 (CRF1R) in complex with the antagonist CP-376395 in a hexagonal setting with translational non-crystallographic symmetry
ComponentsCorticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
KeywordsSIGNALING PROTEIN / 7TM / GPCR / FAMILY B / G-PROTEIN / MEMBRANE / MEMBRANE PROTEIN / RECEPTOR / tNCS / HEXAGONAL
Function / homology
Function and homology information


regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway / corticotropin-releasing hormone binding / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor activity / corticotropin secretion / general adaptation syndrome, behavioral process / parturition / cellular response to corticotropin-releasing hormone stimulus / negative regulation of voltage-gated calcium channel activity ...regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway / corticotropin-releasing hormone binding / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor activity / corticotropin secretion / general adaptation syndrome, behavioral process / parturition / cellular response to corticotropin-releasing hormone stimulus / negative regulation of voltage-gated calcium channel activity / behavioral response to ethanol / cytolysis / fear response / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / exploration behavior / adrenal gland development / viral release from host cell by cytolysis / activation of adenylate cyclase activity / peptidoglycan catabolic process / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (s) signalling events / host cell cytoplasm / cell surface receptor signaling pathway / endosome / defense response to bacterium / neuron projection / immune response / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, corticotropin releasing factor receptor, type 1 / GPCR, family 2, corticotropin releasing factor receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site ...GPCR, family 2, corticotropin releasing factor receptor, type 1 / GPCR, family 2, corticotropin releasing factor receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-1Q5 / OLEIC ACID / Endolysin / Corticotropin-releasing factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB51 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.183 Å
AuthorsDore, A.S. / Bortolato, A. / Hollenstein, K. / Cheng, R.K.Y. / Read, R.J. / Marshall, F.H.
CitationJournal: Curr Mol Pharmacol / Year: 2017
Title: Decoding Corticotropin-Releasing Factor Receptor Type 1 Crystal Structures.
Authors: Dore, A.S. / Bortolato, A. / Hollenstein, K. / Cheng, R.K.Y. / Read, R.J. / Marshall, F.H.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
B: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
C: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,02419
Polymers151,9323
Non-polymers4,09216
Water00
1
A: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0107
Polymers50,6441
Non-polymers1,3666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8185
Polymers50,6441
Non-polymers1,1744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1967
Polymers50,6441
Non-polymers1,5526
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.359, 189.359, 88.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1 / CRFR-1 / Corticotropin-releasing hormone receptor 1


Mass: 50643.855 Da / Num. of mol.: 3
Mutation: V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A,V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, ...Mutation: V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A,V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A,V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A
Source method: isolated from a genetically manipulated source
Details: CORTICOTROPIN-RELEASING FACTOR RECEPTOR 1, T4-LYSOZYME CHIMERIC CONSTRUCT
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB51 (virus)
Gene: CRHR1, CRFR, CRFR1, CRHR, e, RB51ORF131 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34998, UniProt: C3V2B5, lysozyme
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-1Q5 / 3,6-dimethyl-N-(pentan-3-yl)-2-(2,4,6-trimethylphenoxy)pyridin-4-amine


Mass: 326.476 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N2O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.37 % / Description: hexagonal prisms
Crystal growTemperature: 295.6 K / Method: lipidic cubic phase / pH: 5.5
Details: 30% (V/V) PEG 400, 0.2M LITHIUM SULPHATE, 0.1M SODIUM CITRATE 5.5
PH range: 5.3 - 5.7 / Temp details: None

-
Data collection

DiffractionMean temperature: 200 K / Ambient temp details: None
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2012
RadiationMonochromator: Graphite Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.12
ReflectionResolution: 3.18→45.48 Å / Num. obs: 28527 / % possible obs: 93.7 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.094 / Net I/σ(I): 6.4 / Num. measured all: 109312 / Scaling rejects: 49
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.18-3.382.50.721.81028340330.0890.48182
9.55-45.484.90.06822.5557911390.9950.03296.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASERphasing
PHENIX1.8.1refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K5Y

4k5y


Resolution: 3.183→19.91 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.78 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 1528 5.38 %Random Selection
Rwork0.2444 26923 --
obs0.2467 28393 93.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.91 Å2 / Biso mean: 90.6062 Å2 / Biso min: 19.8 Å2
Refinement stepCycle: final / Resolution: 3.183→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 264 0 10244
Biso mean--85.53 --
Num. residues----1239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610476
X-RAY DIFFRACTIONf_angle_d0.88214150
X-RAY DIFFRACTIONf_chiral_restr0.0581579
X-RAY DIFFRACTIONf_plane_restr0.0041725
X-RAY DIFFRACTIONf_dihedral_angle_d15.1663802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1855-3.29890.411250.34542245237075
3.2989-3.43030.36571500.32352574272485
3.4303-3.58550.32491280.30392644277288
3.5855-3.77320.34151440.28352688283289
3.7732-4.00770.31361500.2522760291091
4.0077-4.3140.26281320.23792749288191
4.314-4.74250.22361560.2222778293491
4.7425-5.41590.28761460.22532793293992
5.4159-6.77550.34151770.26422814299192
6.7755-19.50210.21981490.18582878302792
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)
10.09450.0311-0.05810.0154-0.0241-0.02030.0731-0.52040.0064-0.04580.20610.0581-0.01050.1789-00.39460.02250.07890.0013-0.03690.40643.179427.4007-16.6845
2-0.02280.0534-0.07430.01530.00240.03090.18820.15580.01030.1009-0.1175-0.03920.037-0.1268-00.6331-0.0711-0.04550.56230.07080.529416.65936.883-60.8924
30.04570.04690.0060.0334-0.0437-0.0020.17250.02450.24620.05730.1296-0.1576-0.0172-0.112400.4479-0.0122-0.02250.3913-0.01260.357912.809337.1125-24.201
40.09560.00710.01420.028-0.0130.00190.12280.00130.0761-0.07780.15220.0379-0.037-0.1774-00.48540.06210.00670.3901-0.02620.415-4.481938.3129-23.1868
50.0527-0.05070.04220.0695-0.0517-0.00670.11360.03890.066-0.06110.28810.04340.0915-0.0149-00.4926-0.0088-0.09390.35690.03040.3816-7.930485.3426-32.8259
60.21820.0356-0.0597-0.0055-0.14730.0643-0.0263-0.06450.0392-0.05530.00660.104-0.0184-0.0264-00.54870.114-0.08510.4367-0.07190.4557.297772.1673.2134
70.02350.03380.01280.03250.04490.00120.29110.1613-0.2183-0.17160.1489-0.0189-0.0647-0.2188-00.6294-0.0614-0.17950.3251-0.1090.5045-0.050167.2093-31.9623
80.0331-0.0009-0.0090.0215-0.01760.0005-0.10720.0728-0.12860.04640.02680.0573-0.0068-0.039200.5703-0.027-0.17250.3995-0.0230.6136-15.628274.7186-21.8025
90.0073-0.0257-0.00570.014-0.02830.02150.23810.0758-0.14110.10960.14390.32310.0292-0.27170-0.49490.3309-0.55850.0480.36310.0687-25.8254100.8025-31.013
10-0.03020.0144-0.01250.02110.01840.01510.26850.1651-0.00730.03980.2519-0.0418-0.01460.077300.4555-0.7807-0.00880.56880.65730.7823-34.706772.93458.6884
110.11610.0672-0.08020.14860.01430.04210.1031-0.0637-0.0697-0.04440.07680.1724-0.12240.0725-00.4751-0.0745-0.11930.52470.09340.4858-28.096189.6924-4.9501
120.05250.0235-0.02410.0421-0.02190.00610.0162-0.0517-0.0397-0.0878-0.11220.14560.019-0.0365-00.2639-0.1004-0.05710.68420.10860.444-37.1369106.1556-24.3918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 217 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 1155 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1156 through 303 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 372 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 113 through 185 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 186 through 237 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 238 through 296 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 297 through 372 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 112 through 217 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 218 through 1080 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 1081 through 303 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 304 through 370 )C0

+
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