[English] 日本語
Yorodumi
- PDB-7vr5: Crystal structure of CmABCB1 W114Y/W161Y/W363Y/W364Y/M391W (4WY/M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vr5
TitleCrystal structure of CmABCB1 W114Y/W161Y/W363Y/W364Y/M391W (4WY/M391W) mutant
ComponentsProbable ATP-dependent transporter ycf16
KeywordsTRANSPORT PROTEIN / Multi-Drug Transporter ABC Transporter
Function / homology
Function and homology information


oligopeptide export from mitochondrion / ABC-type oligopeptide transporter activity / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable ATP-dependent transporter ycf16
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsInoue, Y. / Ogawa, H. / Kato, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K22495 Japan
Japan Society for the Promotion of Science (JSPS)20H03222 Japan
Japan Society for the Promotion of Science (JSPS)21K19333 Japan
CitationJournal: Protein Sci. / Year: 2022
Title: Structure-based alteration of tryptophan residues of the multidrug transporter CmABCB1 to assess substrate binding using fluorescence spectroscopy.
Authors: Inoue, Y. / Yamaguchi, T. / Otsuka, T. / Utsunomiya, Y. / Pan, D. / Ogawa, H. / Kato, H.
History
DepositionOct 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable ATP-dependent transporter ycf16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2884
Polymers66,2011
Non-polymers1,0873
Water21612
1
A: Probable ATP-dependent transporter ycf16
hetero molecules

A: Probable ATP-dependent transporter ycf16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,5768
Polymers132,4012
Non-polymers2,1756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area12910 Å2
ΔGint-91 kcal/mol
Surface area52760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.570, 179.570, 158.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

-
Components

#1: Protein Probable ATP-dependent transporter ycf16


Mass: 66200.680 Da / Num. of mol.: 1 / Mutation: W114Y,W161Y,W363Y,W364Y,M391W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / Gene: CYME_CMD148C / Plasmid: PPICZ-A / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: M1VAN7
#2: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15.2% PEG 2000 MME, 100 mM potassium nitrate, 100 mM magnesium nitrate, 0.07 mM clotrimazole

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19770 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 100.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.118 / Net I/σ(I): 13.42
Reflection shellResolution: 3→3.16 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 2819 / CC1/2: 0.926 / Rrim(I) all: 0.771 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6N

6a6n


Resolution: 3→15.97 Å / SU ML: 0.4396 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 31.5907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 1004 5.12 %
Rwork0.2132 18618 -
obs0.2157 19622 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.49 Å2
Refinement stepCycle: LAST / Resolution: 3→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 57 12 4556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244626
X-RAY DIFFRACTIONf_angle_d0.49926267
X-RAY DIFFRACTIONf_chiral_restr0.0378732
X-RAY DIFFRACTIONf_plane_restr0.0038797
X-RAY DIFFRACTIONf_dihedral_angle_d11.07321648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.35841320.32512648X-RAY DIFFRACTION99.93
3.16-3.350.3381540.2892618X-RAY DIFFRACTION99.96
3.35-3.610.27941410.24722630X-RAY DIFFRACTION99.89
3.61-3.970.31731340.23272661X-RAY DIFFRACTION99.96
3.97-4.530.27961390.19942659X-RAY DIFFRACTION100
4.53-5.660.22191460.20682676X-RAY DIFFRACTION100
5.67-15.970.24161580.18552726X-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)
14.32565997195-3.48479991178-1.193584386936.609341386561.301905358010.837821150295-0.0407591346701-0.562665532684-0.626508379744-1.01838838565-0.403671342419-0.9156410575830.5059436039610.2114276871330.3574120454041.302315242910.4156391264080.5280869237570.8934413667680.4182930563551.1630488012131.364484063326.902094000736.4141139511
21.94454657799-2.216830073311.902709533491.52517778764-1.654964268471.87137699117-1.18261766051-0.6382956380790.4670473510152.22071357378-0.235938360946-2.04435773062-0.6603232912730.7450104333670.544783885931.360337670330.2344698338840.25642821091.042147978670.3637017412261.0632451182447.636041650151.739726269629.7388596781
33.91963383444-4.453311673050.7848154007083.20634892621-1.837688070422.36414275058-1.27081035883-0.804155994969-0.299246156910.5869241577040.810059382867-1.191974948470.7374120110770.2904567753460.3407774693711.363159443510.4598618617070.2136231169740.9262265590130.243189524761.0989155346755.866635517443.144047546325.8208567502
42.38809484217-2.47628722626-0.631951234374.5614653524-0.09438187422441.43114556339-0.0882471810044-0.133959134770.401949395849-0.0349173053693-0.0472476423076-0.5176734021890.3397365858230.1087616776070.09533760808720.647296127322-0.006613842186460.01236540829810.6148416397390.0757691363610.6688204509359.3768798690558.211559572441.7795398901
58.19227983537-3.346393889161.826709292553.514609055344.200786140898.629056859330.1013671408841.009079565450.534695778989-1.39225180496-0.323756339132-0.0221335963624-0.6002440634130.7234569024930.1662731526951.05675492934-0.0376093816768-0.1045044396450.7774822022560.08433394364060.941640584116-6.1371555761865.955212479827.8588773028
63.11337225227-0.461573147951-2.117067561945.41716059793-4.844989015746.73910826942-0.01688999419081.097083222861.381227750580.2841148753370.426583988340.634172475622-0.757337317578-0.594531012814-0.4095156587680.6991398784410.0803023122261-0.06797562952050.8458602815450.105211844521.37332479757-5.0619319296187.028851149537.3008068217
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 101 through 258 )101 - 2581 - 158
22chain 'A' and (resid 259 through 317 )259 - 317159 - 217
33chain 'A' and (resid 318 through 370 )318 - 370218 - 270
44chain 'A' and (resid 371 through 575 )371 - 575271 - 475
55chain 'A' and (resid 576 through 631 )576 - 631476 - 531
66chain 'A' and (resid 632 through 688 )632 - 688532 - 588

+
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