Journal: Nat Struct Mol Biol / Year: 2013 Title: Full-length Gα(q)-phospholipase C-β3 structure reveals interfaces of the C-terminal coiled-coil domain. Authors: Angeline M Lyon / Somnath Dutta / Cassandra A Boguth / Georgios Skiniotis / John J G Tesmer / Abstract: Phospholipase C-β (PLCβ) is directly activated by Gαq, but the molecular basis for how its distal C-terminal domain (CTD) contributes to maximal activity is poorly understood. Herein we present ...Phospholipase C-β (PLCβ) is directly activated by Gαq, but the molecular basis for how its distal C-terminal domain (CTD) contributes to maximal activity is poorly understood. Herein we present both the crystal structure and cryo-EM three-dimensional reconstructions of human full-length PLCβ3 in complex with mouse Gαq. The distal CTD forms an extended monomeric helical bundle consisting of three antiparallel segments with structural similarity to membrane-binding bin-amphiphysin-Rvs (BAR) domains. Sequence conservation of the distal CTD suggests putative membrane and protein interaction sites, the latter of which bind the N-terminal helix of Gαq in both the crystal structure and cryo-EM reconstructions. Functional analysis suggests that the distal CTD has roles in membrane targeting and in optimizing the orientation of the catalytic core at the membrane for maximal rates of lipid hydrolysis.
Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
CHAIN E IS MOST LIKELY A C-TERMINAL PART OF EITHER CHAIN B OR CHAIN D IN THE CRYSTAL STRUCTURE. ...CHAIN E IS MOST LIKELY A C-TERMINAL PART OF EITHER CHAIN B OR CHAIN D IN THE CRYSTAL STRUCTURE. THERE IS NOT ENOUGH ELECTRON DENSITY TO ASSIGN IT TO CHAIN B OR CHAIN D.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal grow
Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 100 mM MES pH 6.75, 100-200 mM NaCl, and 11-12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution: 4→19.99 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / SU B: 102.082 / SU ML: 0.575 / Cross valid method: THROUGHOUT / ESU R Free: 0.88 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25468
1715
5 %
RANDOM
Rwork
0.21386
-
-
-
obs
0.21588
32433
77.78 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 113.58 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.07 Å2
0 Å2
0 Å2
2-
-
0.04 Å2
0 Å2
3-
-
-
0.03 Å2
Refinement step
Cycle: LAST / Resolution: 4→19.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
19688
0
70
6
19764
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.019
20159
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
14200
X-RAY DIFFRACTION
r_angle_refined_deg
0.858
1.976
27244
X-RAY DIFFRACTION
r_angle_other_deg
0.75
3
34456
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.27
5
2418
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.929
23.796
1001
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.893
15
3677
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.068
15
183
X-RAY DIFFRACTION
r_chiral_restr
0.049
0.2
2991
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
22145
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
4146
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
2550
MEDIUMPOSITIONAL
0.01
0.5
1
A
1915
TIGHTTHERMAL
3.57
0.5
1
A
2550
MEDIUMTHERMAL
3.96
2
2
B
5795
MEDIUMPOSITIONAL
0.01
0.5
2
B
4330
TIGHTTHERMAL
4.06
0.5
2
B
5795
MEDIUMTHERMAL
4.72
2
LS refinement shell
Resolution: 4→4.1 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.355
96
-
Rwork
0.367
1773
-
obs
-
-
63.04 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
2.9064
0.2513
-0.0939
2.7306
0.4003
2.2834
0.0514
0.1545
0.6261
0.0907
0.1275
-0.1329
-0.1573
0.007
-0.1789
0.4218
0.0085
0.1444
0.0154
0.0457
0.3585
-25.3596
36.7047
-55.6075
2
2.8009
0.4391
-0.5256
2.6194
-1.3995
2.3973
0.0907
-0.3207
0.653
-0.0014
-0.0499
0.1476
0.0163
0.0756
-0.0408
0.3077
-0.0586
0.0939
0.0472
-0.108
0.3769
-65.3862
19.2101
74.1339
3
2.1292
0.0915
-0.3858
1.9219
-0.4141
2.1116
-0.0446
-0.4552
-0.1344
0.1635
-0.0441
-0.0186
-0.0301
0.0302
0.0887
0.1398
-0.0042
-0.0059
0.1011
0.02
0.1
-39.7017
6.7677
-29.2356
4
1.9123
0.348
-0.1018
2.2762
0.2442
2.7343
-0.0662
0.5408
-0.0703
-0.215
0.0886
-0.1233
0.1165
0.2517
-0.0224
0.2356
0.0261
-0.0604
0.1926
-0.02
0.1372
-46.5114
-3.6061
43.2348
5
1.3442
0.9056
-0.8518
1.4262
-1.0178
0.8858
-0.0749
0.2537
-0.6208
-0.1366
-0.1035
-0.2623
0.3247
-0.1542
0.1784
0.7844
-0.1936
0.1199
0.6087
-0.0818
1.3003
-42.0228
57.6086
-99.1521
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
19 - 354
2
X-RAY DIFFRACTION
1
A
401 - 403
3
X-RAY DIFFRACTION
1
A
501 - 503
4
X-RAY DIFFRACTION
1
B
863 - 881
5
X-RAY DIFFRACTION
2
C
35 - 355
6
X-RAY DIFFRACTION
2
C
401 - 403
7
X-RAY DIFFRACTION
2
C
501 - 503
8
X-RAY DIFFRACTION
2
D
863 - 881
9
X-RAY DIFFRACTION
3
B
11 - 862
10
X-RAY DIFFRACTION
3
B
1301
11
X-RAY DIFFRACTION
4
D
10 - 862
12
X-RAY DIFFRACTION
4
D
1301
13
X-RAY DIFFRACTION
5
E
934 - 1192
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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