[English] 日本語
Yorodumi
- PDB-7w7s: High resolution structure of a fish aquaporin reveals a novel ext... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w7s
TitleHigh resolution structure of a fish aquaporin reveals a novel extracellular fold.
ComponentsAquaporin 1
KeywordsMEMBRANE PROTEIN / Aquaporin / fish / Anabas testudineus / Pichia pastoris / transport protein
Function / homologyAquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / channel activity / membrane / Aquaporin 1
Function and homology information
Biological speciesAnabas testudineus (climbing perch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZeng, J. / Schmitz, F. / Isaksson, S. / Glas, J. / Arbab, O. / Andersson, M. / Sundell, K. / Eriksson, L. / Swaminathan, K. / Tornroth-Horsefield, S. / Hedfalk, K.
Funding support Sweden, Singapore, 6items
OrganizationGrant numberCountry
Swedish Research CouncilK2013-66X-20431-07-05 Sweden
Swedish Research Council2009-00360 Sweden
Swedish Research Council2013-05945 Sweden
Ministry of Education (MoE, Singapore)R154-000-632-112 Singapore
National Research Foundation (NRF, Singapore)R706-000-041-279 Sweden
Swedish Research Council FORMAS2012-771 Sweden
CitationJournal: Life Sci Alliance / Year: 2022
Title: High-resolution structure of a fish aquaporin reveals a novel extracellular fold.
Authors: Zeng, J. / Schmitz, F. / Isaksson, S. / Glas, J. / Arbab, O. / Andersson, M. / Sundell, K. / Eriksson, L.A. / Swaminathan, K. / Tornroth-Horsefield, S. / Hedfalk, K.
History
DepositionDec 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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: Aquaporin 1


Theoretical massNumber of molelcules
Total (without water)25,5521
Polymers25,5521
Non-polymers00
Water2,234124
1
A: Aquaporin 1

A: Aquaporin 1

A: Aquaporin 1

A: Aquaporin 1


Theoretical massNumber of molelcules
Total (without water)102,2074
Polymers102,2074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Buried area10780 Å2
ΔGint-100 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.060, 80.060, 95.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-386-

HOH

-
Components

#1: Protein Aquaporin 1 / Aquaporin 1aa


Mass: 25551.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabas testudineus (climbing perch) / Gene: aqp1aa, aqp1 / Production host: Komagataella pastoris (fungus) / References: UniProt: M1K561
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: reservoir solution: 0.1M Tris-HCl (pH 7.8). 5% w/v gamma-PGA (Na+ form, LM), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed ...Details: reservoir solution: 0.1M Tris-HCl (pH 7.8). 5% w/v gamma-PGA (Na+ form, LM), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed with 1 micro liter 30% w/v D-Sorbitol. Crystallization drops were set up by mixing the reservoir/additive mixture with protein at 1:1 or 2:1 ratio and the drops were left to equilibrate against 0.5 milliliter reservoir at room temperature and crystal grew in cold room (4 degree)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.9→95.28 Å / Num. all: 25108 / Num. obs: 25108 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 25.19 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.114 / Rsym value: 0.108 / Net I/av σ(I): 1.3 / Net I/σ(I): 15.1 / Num. measured all: 305910
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs
1.9-212.10.6571.24358735880.1950.6860.6574
2-2.1212.90.5351.54351533770.1550.5570.5355.1
2.12-2.2712.30.39523970832330.1170.4130.3956.6
2.27-2.4511.70.25633509729950.0780.2680.2569.4
2.45-2.6912.80.1754.33537527610.0510.1820.17513.4
2.69-312.10.1275.93062725360.0380.1330.12717.4
3-3.4712.30.07992743022370.0230.0820.07925
3.47-4.2512.20.05312.12359119270.0160.0550.05335.3
4.25-6.0111.40.04712.41747915300.0150.050.04737.8
6.01-95.2810.30.0661.295019240.0330.0760.06637.5

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J4N

1j4n


Resolution: 1.9→61.294 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1305 5.2 %
Rwork0.1779 23773 -
obs0.1792 25078 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.35 Å2 / Biso mean: 36.3923 Å2 / Biso min: 14.03 Å2
Refinement stepCycle: final / Resolution: 1.9→61.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 0 124 1718
Biso mean---47.51 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141623
X-RAY DIFFRACTIONf_angle_d1.1712207
X-RAY DIFFRACTIONf_chiral_restr0.086269
X-RAY DIFFRACTIONf_plane_restr0.01275
X-RAY DIFFRACTIONf_dihedral_angle_d10.228948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.97610.27631330.27992594
1.9761-2.0660.29261310.23522591
2.066-2.1750.21171540.19672593
2.175-2.31120.1981470.16462591
2.3112-2.48970.17431590.13862607
2.4897-2.74020.16711360.13722629
2.7402-3.13670.18381460.14892633
3.1367-3.95190.20011400.16052692
3.9519-61.2940.20081590.19822843
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)
17.79380.206-5.25163.314-0.30448.12920.3004-0.53540.34280.33-0.08880.616-0.4429-0.1876-0.28710.19020.00640.02160.2395-0.05730.42615.18885.89225.69
24.9271.1803-2.78630.4668-1.16952.945-1.01861.3622-0.1363-1.46560.6461.32130.0607-0.52950.37221.1032-0.2451-0.6360.85920.03032.324430.09281.3020.624
31.99690.3020.0071.72340.58682.3838-0.0139-0.19140.04830.0163-0.09220.3312-0.0849-0.32090.0730.1301-0.00040.01740.1836-0.01380.319518.99879.87122.782
45.445-5.7959-4.87686.82184.93934.4670.09840.40310.9677-1.4301-0.20210.2435-1.0284-0.3743-0.01090.45550.0276-0.17980.2586-0.01470.502219.63274.112.946
52.66260.17151.79171.06790.25972.79390.0585-0.2275-0.09990.055-0.02260.14960.1985-0.3126-0.0650.1352-0.02360.01940.15030.00880.265422.37269.9719.746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:33 )A2 - 33
2X-RAY DIFFRACTION2( CHAIN A AND RESID 34:43 )A34 - 43
3X-RAY DIFFRACTION3( CHAIN A AND RESID 44:108 )A44 - 108
4X-RAY DIFFRACTION4( CHAIN A AND RESID 114:127 )A114 - 127
5X-RAY DIFFRACTION5( CHAIN A AND RESID 128:226 )A128 - 226

+
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