[English] 日本語
Yorodumi
- PDB-6b73: Crystal Structure of a nanobody-stabilized active state of the ka... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b73
TitleCrystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor
Components
  • NanobodySingle-domain antibody
  • Soluble cytochrome b562, kappa-type opioid receptor
KeywordsMEMBRANE PROTEIN/AGONIST / GPCR / opioid receptor / addiction / active state / nanobody / structure-function / morphinan / LCP / membrane protein / MEMBRANE PROTEIN-AGONIST complex
Function / homology
Function and homology information


dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / negative regulation of luteinizing hormone secretion / positive regulation of eating behavior / sensory perception of temperature stimulus / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / conditioned place preference / G protein-coupled opioid receptor signaling pathway ...dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / negative regulation of luteinizing hormone secretion / positive regulation of eating behavior / sensory perception of temperature stimulus / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / conditioned place preference / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion / sensory perception / positive regulation of potassium ion transmembrane transport / maternal behavior / neuropeptide binding / receptor serine/threonine kinase binding / positive regulation of p38MAPK cascade / eating behavior / behavioral response to cocaine / estrous cycle / neuropeptide signaling pathway / axon terminus / MECP2 regulates neuronal receptors and channels / sensory perception of pain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / electron transport chain / locomotory behavior / cellular response to glucose stimulus / response to insulin / synaptic vesicle membrane / response to estrogen / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / perikaryon / chemical synaptic transmission / postsynaptic membrane / response to ethanol / defense response to virus / cellular response to lipopolysaccharide / electron transfer activity / periplasmic space / neuron projection / immune response / iron ion binding / dendrite / heme binding / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Kappa opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Kappa opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Chem-CVV / OLEIC ACID / Soluble cytochrome b562 / Kappa-type opioid receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChe, T. / Majumdar, S. / Zaidi, S.A. / Kormos, C. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. ...Che, T. / Majumdar, S. / Zaidi, S.A. / Kormos, C. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. / Han, G.W. / Lee, M.Y. / Pardon, E. / Steyaert, J. / Huang, X.P. / Strachan, R.T. / Tribo, A.R. / Pasternak, G.W. / Carroll, I.F. / Stevens, R.C. / Cherezov, V. / Katritch, V. / Wacker, D. / Roth, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1MH61887, U19MH82441 United States
CitationJournal: Cell / Year: 2018
Title: Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor.
Authors: Che, T. / Majumdar, S. / Zaidi, S.A. / Ondachi, P. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. / Han, G.W. / Lee, M.Y. / Pardon, E. / Steyaert, J. / ...Authors: Che, T. / Majumdar, S. / Zaidi, S.A. / Ondachi, P. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. / Han, G.W. / Lee, M.Y. / Pardon, E. / Steyaert, J. / Huang, X.P. / Strachan, R.T. / Tribo, A.R. / Pasternak, G.W. / Carroll, F.I. / Stevens, R.C. / Cherezov, V. / Katritch, V. / Wacker, D. / Roth, B.L.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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: Soluble cytochrome b562, kappa-type opioid receptor
B: Soluble cytochrome b562, kappa-type opioid receptor
C: Nanobody
D: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0519
Polymers123,8874
Non-polymers2,1655
Water0
1
A: Soluble cytochrome b562, kappa-type opioid receptor
D: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1675
Polymers61,9432
Non-polymers1,2243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area19360 Å2
MethodPISA
2
B: Soluble cytochrome b562, kappa-type opioid receptor
C: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8844
Polymers61,9432
Non-polymers9412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-15 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.310, 150.750, 100.280
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

-
Components

#1: Protein Soluble cytochrome b562, kappa-type opioid receptor / Cytochrome b-562 / KOR-1


Mass: 47030.043 Da / Num. of mol.: 2 / Fragment: unp residues 23-128; unp residues 54-358 / Mutation: M29W, H124I, L51R, I135L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, OPRK1, OPRK / Production host: unidentified baculovirus / References: UniProt: P0ABE7, UniProt: P41145
#2: Antibody Nanobody / Single-domain antibody


Mass: 14913.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama)
#3: Chemical ChemComp-CVV / N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide


Mass: 554.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27IN2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Bis-tris pH 6.5-7.0, 140-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese(II) chloride tetrahydrate, 28-30% PEG400

-
Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→46.94 Å / Num. obs: 30278 / % possible obs: 93.6 % / Redundancy: 3 % / Biso Wilson estimate: 78.82 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.187 / Net I/σ(I): 4
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4159 / CC1/2: 0.537 / % possible all: 88.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4DJH, 5C1M, 1M6T

4djh

5c1m

1m6t


Resolution: 3.1→46.94 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.832 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.834 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.714 / SU Rfree Blow DPI: 0.374 / SU Rfree Cruickshank DPI: 0.391
Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED ABOVE THE LIGAND BINDING SITE AND NEAR THE TRP222 ON BOTH A AND B CHAINS. THEY HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1505 4.97 %RANDOM
Rwork0.254 ---
obs0.255 30255 93.5 %-
Displacement parametersBiso mean: 85.74 Å2
Baniso -1Baniso -2Baniso -3
1--29.6548 Å20 Å2-3.2357 Å2
2--21.5032 Å20 Å2
3---8.1516 Å2
Refine analyzeLuzzati coordinate error obs: 0.6 Å
Refinement stepCycle: 1 / Resolution: 3.1→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 0 136 0 6142
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016307HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.958661HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2728SINUSOIDAL15
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes931HARMONIC5
X-RAY DIFFRACTIONt_it6307HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion1.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion901SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7781SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.283 138 5.1 %
Rwork0.245 2570 -
all0.247 2708 -
obs--85.61 %
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)
10.6808-0.1949-0.33772.56820.97591.69360.0929-0.1566-0.0532-0.17170.00230.02080.0122-0.0852-0.09520.0608-0.0397-0.0984-0.15670.0077-0.190861.2141-21.98665.1559
20.7626-0.37080.11392.12480.64491.00440.04180.1213-0.06410.286-0.0921-0.029-0.0033-0.10520.05030.1822-0.0208-0.0436-0.16970.0206-0.237856.746513.9345-5.7761
34.81171.64141.12.9341.09744.7865-0.0681-0.07280.3412-0.09630.04420.1442-0.2113-0.01970.02390.05410.06-0.0929-0.17860.0343-0.225149.95343.0159-40.5571
42.7839-2.0803-2.09083.41031.88076.155-0.01910.0475-0.27380.25290.14270.0658-0.0334-0.0208-0.12370.1137-0.0409-0.0531-0.22780.0609-0.244253.6609-9.703539.7407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|51 - A|339 }
2X-RAY DIFFRACTION2{ B|54 - B|334 }
3X-RAY DIFFRACTION3{ C|4 - C|129 }
4X-RAY DIFFRACTION4{ D|4 - D|129 }

+
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