[English] 日本語
Yorodumi
- PDB-6nlo: Human ABCC6 NBD1 H812A in Apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nlo
TitleHuman ABCC6 NBD1 H812A in Apo state
ComponentsMultidrug resistance-associated protein 6
KeywordsTRANSPORT PROTEIN / ABCC6 / NBD1 / Apo state / ATP-Binding Cassette transporter C6 / nucleotide binding domain 1
Function / homology
Function and homology information


Defective ABCC6 causes PXE / inorganic diphosphate transport / ATP transport / inhibition of non-skeletal tissue mineralization / leukotriene transport / intracellular phosphate ion homeostasis / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / response to sodium phosphate / ATPase-coupled inorganic anion transmembrane transporter activity ...Defective ABCC6 causes PXE / inorganic diphosphate transport / ATP transport / inhibition of non-skeletal tissue mineralization / leukotriene transport / intracellular phosphate ion homeostasis / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / response to sodium phosphate / ATPase-coupled inorganic anion transmembrane transporter activity / phosphate ion homeostasis / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / response to magnesium ion / ATPase-coupled transmembrane transporter activity / calcium ion homeostasis / ATP metabolic process / visual perception / basal plasma membrane / ABC-family proteins mediated transport / transmembrane transport / gene expression / basolateral plasma membrane / response to xenobiotic stimulus / endoplasmic reticulum membrane / ATP hydrolysis activity / extracellular region / nucleoplasm / ATP binding / membrane / plasma membrane
Similarity search - Function
Multi drug resistance-associated protein / 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. ...Multi drug resistance-associated protein / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-binding cassette sub-family C member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85021981416 Å
AuthorsZheng, A. / Thibodeau, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122091 United States
CitationJournal: To be published
Title: Structures of human ABCC6 NBD1 and NBD2
Authors: Zheng, A. / Thibodeau, P.H.
History
DepositionJan 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Multidrug resistance-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3382
Polymers25,2421
Non-polymers961
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 92.600, 45.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Multidrug resistance-associated protein 6 / ATP-binding cassette sub-family C member 6 / Anthracycline resistance-associated protein / Multi- ...ATP-binding cassette sub-family C member 6 / Anthracycline resistance-associated protein / Multi-specific organic anion transporter E / MOAT-E


Mass: 25241.824 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain 1, residues 622-859 / Mutation: M848V, H812A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCC6, ARA, MRP6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95255
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 2.1-2.4M Ammonium Sulfate 0.1M HEPES pH 6.8-8.2 / PH range: 6.8-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.85→39.581 Å / Num. obs: 5467 / % possible obs: 99.9 % / Redundancy: 19.41 % / Biso Wilson estimate: 53.6577065481 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.047 / Rrim(I) all: 0.209 / Net I/σ(I): 15.32
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 10.66 % / Rmerge(I) obs: 1.474 / Mean I/σ(I) obs: 2 / Num. unique obs: 541 / CC1/2: 0.765 / Rpim(I) all: 0.474 / Rrim(I) all: 1.55 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Coot0.8.8model building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZS

6bzs


Resolution: 2.85021981416→39.5805684083 Å / SU ML: 0.356837989154 / Cross valid method: FREE R-VALUE / σ(F): 1.47636511379 / Phase error: 25.2360877641
RfactorNum. reflection% reflection
Rfree0.259750519508 544 9.97798972854 %
Rwork0.229303242172 --
obs0.232547704813 5452 99.8900696226 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.1407473374 Å2
Refinement stepCycle: LAST / Resolution: 2.85021981416→39.5805684083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 5 0 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004566432059781733
X-RAY DIFFRACTIONf_angle_d0.7660257737682364
X-RAY DIFFRACTIONf_chiral_restr0.0489093270488279
X-RAY DIFFRACTIONf_plane_restr0.00553225835177305
X-RAY DIFFRACTIONf_dihedral_angle_d10.2357732791027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8502-3.13690.3306400854941330.2986309197491211X-RAY DIFFRACTION100
3.1369-3.59060.3145862158131340.2500396819111209X-RAY DIFFRACTION99.9255952381
3.5906-4.52280.2533862059881370.211031000661224X-RAY DIFFRACTION100
4.5228-39.58440.2169178071311400.2125093605561264X-RAY DIFFRACTION99.645138396

+
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