- PDB-1u4e: Crystal Structure of Cytoplasmic Domains of GIRK1 channel -
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Basic information
Entry
Database: PDB / ID: 1u4e
Title
Crystal Structure of Cytoplasmic Domains of GIRK1 channel
Components
G protein-activated inward rectifier potassium channel 1
Keywords
METAL TRANSPORT
Function / homology
Function and homology information
: / G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / voltage-gated potassium channel complex ...: / G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / voltage-gated potassium channel complex / response to electrical stimulus / T-tubule / presynaptic membrane / external side of plasma membrane / cell surface / plasma membrane Similarity search - Function
Journal: Nat Neurosci / Year: 2005 Title: Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification. Authors: Scott Pegan / Christine Arrabit / Wei Zhou / Witek Kwiatkowski / Anthony Collins / Paul A Slesinger / Senyon Choe / Abstract: N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. ...N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. Two new crystal structures of the cytoplasmic domains of Kir2.1 (Kir2.1(L)) and the G protein-sensitive Kir3.1 (Kir3.1(S)) channels in the absence of PIP(2) show the cytoplasmic ion-permeation pathways occluded by four cytoplasmic loops that form a girdle around the central pore (G-loop). Significant flexibility of the pore-facing G-loop of Kir2.1(L) and Kir3.1(S) suggests a possible role as a diffusion barrier between cytoplasmic and transmembrane pores. Consistent with this, mutations of the G-loop disrupted gating or inward rectification. Structural comparison shows a di-aspartate cluster on the distal end of the cytoplasmic pore of Kir2.1(L) that is important for modulating inward rectification. Taken together, these results suggest the cytoplasmic domains of Kir channels undergo structural changes to modulate gating and inward rectification.
History
Deposition
Jul 24, 2004
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Mar 8, 2005
Provider: repository / Type: Initial release
Revision 1.1
Apr 30, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Derived calculations / Version format compliance
Revision 1.3
Aug 23, 2017
Group: Source and taxonomy / Category: entity_src_gen
Resolution: 2.09→91.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.589 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23505
813
5.1 %
RANDOM
Rwork
0.19431
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-
-
all
0.19641
15270
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-
obs
0.19641
15270
96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 33.928 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.12 Å2
0 Å2
0 Å2
2-
-
-1.12 Å2
0 Å2
3-
-
-
2.23 Å2
Refinement step
Cycle: LAST / Resolution: 2.09→91.29 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1599
0
0
129
1728
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.034
0.021
1632
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1461
X-RAY DIFFRACTION
r_angle_refined_deg
2.378
1.951
2204
X-RAY DIFFRACTION
r_angle_other_deg
1.161
3
3398
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
9.008
5
198
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
X-RAY DIFFRACTION
r_chiral_restr
0.177
0.2
246
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.02
1803
X-RAY DIFFRACTION
r_gen_planes_other
0.005
0.02
340
X-RAY DIFFRACTION
r_nbd_refined
0.234
0.2
305
X-RAY DIFFRACTION
r_nbd_other
0.272
0.2
1720
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
0.098
0.2
992
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.222
0.2
112
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.237
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.377
0.2
79
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.2
0.2
21
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_mcbond_it
1.858
1.5
996
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
3.268
2
1618
X-RAY DIFFRACTION
r_scbond_it
4.212
3
636
X-RAY DIFFRACTION
r_scangle_it
6.655
4.5
586
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.09→2.145 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.322
47
Rwork
0.276
999
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