[English] 日本語
Yorodumi
- PDB-2ptm: Structure and rearrangements in the carboxy-terminal region of Sp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ptm
TitleStructure and rearrangements in the carboxy-terminal region of SpIH channels
ComponentsHyperpolarization-activated (Ih) channel
KeywordsTRANSPORT PROTEIN / ion channel / cyclic nucleotide binding domain / C-linker / cAMP / cGMP / spHCN1 / HCN
Function / homology
Function and homology information


HCN channel complex / regulation of membrane depolarization / voltage-gated potassium channel activity / sodium ion transmembrane transport / potassium ion transmembrane transport / nucleotide binding
Similarity search - Function
Helix hairpin bin / Ion transport N-terminal / Ion transport protein N-terminal / : / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Helix hairpin bin / Ion transport N-terminal / Ion transport protein N-terminal / : / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / COBALT HEXAMMINE(III) / Hyperpolarization-activated (Ih) channel
Similarity search - Component
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsFlynn, G.E. / Black, K.D. / Islas, L.D. / Sankaran, B. / Zagotta, W.N.
CitationJournal: Structure / Year: 2007
Title: Structure and rearrangements in the carboxy-terminal region of SpIH channels.
Authors: Flynn, G.E. / Black, K.D. / Islas, L.D. / Sankaran, B. / Zagotta, W.N.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 28, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details ..._refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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: Hyperpolarization-activated (Ih) channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7833
Polymers23,2931
Non-polymers4902
Water3,675204
1
A: Hyperpolarization-activated (Ih) channel
hetero molecules

A: Hyperpolarization-activated (Ih) channel
hetero molecules

A: Hyperpolarization-activated (Ih) channel
hetero molecules

A: Hyperpolarization-activated (Ih) channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,13212
Polymers93,1704
Non-polymers1,9618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area12000 Å2
ΔGint-47 kcal/mol
Surface area35900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.354, 92.354, 63.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A--

HOH

21A-1-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: Symmetry operation Symm. ID. (Pisa) x,y,z 1_555 -y+1/2,x+1/2,z 3_555 y-1/2,-x+1/2,z 4_455 -x,-y+1,z 2_565

-
Components

#1: Protein Hyperpolarization-activated (Ih) channel


Mass: 23292.576 Da / Num. of mol.: 1 / Fragment: C-terminal region (residues 470-665)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Strongylocentrotus purpuratus (purple sea urchin)
Plasmid: pHMalc2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl-21 (DE3) / References: UniProt: O76977
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 % w/v PEG 6000, 0.5 M NaCl, 20 % glycerol, 0.1 M HEPES, 10 mM hexamine cobalt trichloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97935
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2004
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 21275 / Num. obs: 21201 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 30.44 Å2 / Rsym value: 0.074 / Net I/σ(I): 30.5
Reflection shellResolution: 1.93→2 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 7.9 / Num. unique all: 2077 / Rsym value: 0.3 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1q5o

1q5o


Resolution: 1.93→29.205 Å / FOM work R set: 0.852 / σ(F): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.242 1089 5.14 %
Rwork0.187 --
all-21201 -
obs-21201 99.7 %
Solvent computationBsol: 79.142 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 99.94 Å2 / Biso mean: 41.33 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.473 Å20 Å2-0 Å2
2--1.473 Å20 Å2
3----2.945 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 29 204 1777
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_deg0.6331
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONfHIRAL0.0511
X-RAY DIFFRACTIONf_dihedral_angle_d9.4741
X-RAY DIFFRACTIONfLANE0.0021
X-RAY DIFFRACTIONfonbonded4.2661

+
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