[English] 日本語
Yorodumi
- PDB-6qv0: Structure of ATP-bound outward-facing TM287/288 in complex with s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qv0
TitleStructure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35
Components
  • ABC transporter, ATP-binding protein
  • Sb_TM35
  • Uncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsMEMBRANE PROTEIN / ABC exporter / ABC transporter / Membrane Transporter / sybody / nanobody
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ABC transporter, ATP-binding protein / Uncharacterized ABC transporter ATP-binding protein TM_0288
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.12 Å
AuthorsHutter, C.A.J. / Huerlimann, L.M. / Zimmermann, I. / Egloff, P. / Seeger, M.A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_144823 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: The extracellular gate shapes the energy profile of an ABC exporter.
Authors: Hutter, C.A.J. / Timachi, M.H. / Hurlimann, L.M. / Zimmermann, I. / Egloff, P. / Goddeke, H. / Kucher, S. / Stefanic, S. / Karttunen, M. / Schafer, L.V. / Bordignon, E. / Seeger, M.A.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter, ATP-binding protein
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
C: ABC transporter, ATP-binding protein
D: Uncharacterized ABC transporter ATP-binding protein TM_0288
E: Sb_TM35
F: Sb_TM35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,36414
Polymers293,2386
Non-polymers2,1268
Water00
1
A: ABC transporter, ATP-binding protein
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
E: Sb_TM35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6827
Polymers146,6193
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-122 kcal/mol
Surface area52620 Å2
MethodPISA
2
C: ABC transporter, ATP-binding protein
D: Uncharacterized ABC transporter ATP-binding protein TM_0288
F: Sb_TM35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6827
Polymers146,6193
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18310 Å2
ΔGint-128 kcal/mol
Surface area52960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.280, 77.290, 207.180
Angle α, β, γ (deg.)90.000, 112.550, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ABC transporter, ATP-binding protein


Mass: 65016.781 Da / Num. of mol.: 2 / Fragment: ABC transporter / Mutation: D41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0287 / Plasmid: pBXNH3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061 / References: UniProt: Q9WYC3
#2: Protein Uncharacterized ABC transporter ATP-binding protein TM_0288


Mass: 67758.914 Da / Num. of mol.: 2 / Fragment: ABC transporter / Mutation: D65A, E517A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0288 / Plasmid: pBXNH3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061 / References: UniProt: Q9WYC4
#3: Antibody Sb_TM35


Mass: 13843.184 Da / Num. of mol.: 2 / Fragment: sybody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pBXPHM3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→49.19 Å / Num. obs: 55123 / % possible obs: 62.6 % / Redundancy: 6.726 % / Biso Wilson estimate: 81.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.202 / Χ2: 0.923 / Net I/σ(I): 9.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.11-3.196.5960.942.282030.7721.0213.2
3.19-3.286.7070.77535390.8090.848.5
3.28-3.386.5210.862.548980.7520.93314.7
3.38-3.486.5010.762.9413360.8480.82522.5
3.48-3.596.5580.7672.9718830.8490.83232.8
3.59-3.725.9841.2121.816750.8531.32529.9
3.72-3.866.3590.8362.7438530.9250.91170.9
3.86-4.026.0240.7752.7736580.8930.84771
4.02-4.26.4850.5684.0149410.9490.61899.6
4.2-4.47.2090.4215.5347640.980.45399.6
4.4-4.647.2580.297.4645340.9910.31399.6
4.64-4.927.190.2558.0542830.9930.27599.6
4.92-5.267.0790.2757.7540510.9890.29799.5
5.26-5.686.9880.2967.3237630.9850.3299.7
5.68-6.236.9120.2967.3734740.9750.31999.7
6.23-6.966.5240.1959.931830.9880.21299.7
6.96-8.045.9750.11114.7827720.9930.12299.6
8.04-9.846.6680.04731.1223970.9980.05199.6
9.84-13.927.0310.03741.6418740.9990.0499.9
13.92-49.196.5240.02946.3310420.9990.03295.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→49.19 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.557
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2797 5.07 %RANDOM
Rwork0.244 ---
obs0.245 55122 62.9 %-
Displacement parametersBiso max: 191.43 Å2 / Biso mean: 71.88 Å2 / Biso min: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.8586 Å20 Å2-4.0569 Å2
2---3.6906 Å20 Å2
3----0.168 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: final / Resolution: 3.12→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19958 0 128 0 20086
Biso mean--50.92 --
Num. residues----2529
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7276SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3444HARMONIC5
X-RAY DIFFRACTIONt_it20451HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2727SEMIHARMONIC5
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_contact23714SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20451HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg27707HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion1.78
X-RAY DIFFRACTIONt_other_torsion20.54
LS refinement shellResolution: 3.12→3.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.352 49 4.44 %
Rwork0.2969 1054 -
all0.2989 1103 -
obs--7.17 %
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)
10.32290.05430.47220.5966-0.43843.812-0.07750.10850.03210.0573-0.06660.1012-0.55330.00180.14410.03310.0093-0.0902-0.3096-0.03130.046346.26455.261157.3282
20.53480.11930.64770.0957-0.23494.63920.12890.2929-0.1794-0.192-0.101-0.00470.50730.6437-0.0279-0.04320.1338-0.0489-0.2582-0.098-0.042455.6174-10.716848.9269
30.51160.10990.39240.28340.26571.6671-0.2-0.18050.1017-0.0225-0.02940.0052-0.6257-0.49290.22940.00760.0748-0.10330.0501-0.0455-0.1284-23.313644.979578.5427
40.7446-0.02270.83330.1946-0.00442.74150.08660.0328-0.2544-0.1238-0.0230.00420.0955-0.2255-0.0636-0.1786-0.035-0.0305-0.0735-0.0519-0.011-18.990126.60670.9462
5-1.41934.85923.12441.6051-2.09278.437-0.029-0.01780.37180.15790.0706-0.2243-0.25450.0832-0.04160.3102-0.2606-0.04870.12750.1276-0.45156.771334.0797-14.1308
63.944.20691.00511.392-2.0038.4306-0.04530.01650.2650.18920.045-0.2969-0.16480.13040.00030.1891-0.3935-0.07990.11530.155-0.5098-6.903365.84455.4021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 569
2X-RAY DIFFRACTION2{ B|* }B22 - 591
3X-RAY DIFFRACTION3{ C|* }C1 - 569
4X-RAY DIFFRACTION4{ D|* }D18 - 591
5X-RAY DIFFRACTION5{ E|* }E1 - 124
6X-RAY DIFFRACTION6{ F|* }F1 - 124

+
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