Cell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / rod shape-determining protein MreC / regulation of cell shape / plasma membrane / Cell shape-determining protein MreC
Function and homology information
Biological species
Pseudomonas aeruginosa PAO1 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.471 Å
Journal: Nat Commun / Year: 2021 Title: Self-association of MreC as a regulatory signal in bacterial cell wall elongation. Authors: Alexandre Martins / Carlos Contreras-Martel / Manon Janet-Maitre / Mayara M Miyachiro / Leandro F Estrozi / Daniel Maragno Trindade / Caíque C Malospirito / Fernanda Rodrigues-Costa / ...Authors: Alexandre Martins / Carlos Contreras-Martel / Manon Janet-Maitre / Mayara M Miyachiro / Leandro F Estrozi / Daniel Maragno Trindade / Caíque C Malospirito / Fernanda Rodrigues-Costa / Lionel Imbert / Viviana Job / Guy Schoehn / Ina Attrée / Andréa Dessen / Abstract: The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the ...The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the cytoskeletal element MreB and regulates the activity of cell wall biosynthesis enzymes, in a process that may be dependent on MreC self-association. Here, we use electron cryo-microscopy and X-ray crystallography to determine the structure of a self-associated form of MreC from Pseudomonas aeruginosa in atomic detail. MreC monomers interact in head-to-tail fashion. Longitudinal and lateral interfaces are essential for oligomerization in vitro, and a phylogenetic analysis of proteobacterial MreC sequences indicates the prevalence of the identified interfaces. Our results are consistent with a model where MreC's ability to alternate between self-association and interaction with the cell wall biosynthesis machinery plays a key role in the regulation of elongasome activity.
Method to determine structure: AB INITIO PHASING / Resolution: 1.471→42.435 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.582 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.083 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2445
2036
7.473 %
Rwork
0.2168
25210
-
all
0.219
-
-
obs
-
27246
96.262 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parameters
Biso mean: 39.496 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.658 Å2
0.329 Å2
-0 Å2
2-
-
0.658 Å2
0 Å2
3-
-
-
-2.133 Å2
Refinement step
Cycle: LAST / Resolution: 1.471→42.435 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1178
0
6
66
1250
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.013
1198
X-RAY DIFFRACTION
r_bond_other_d
0.006
0.017
1162
X-RAY DIFFRACTION
r_angle_refined_deg
1.332
1.643
1631
X-RAY DIFFRACTION
r_angle_other_deg
1.292
1.573
2683
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.701
5
154
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.244
21.5
60
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.028
15
198
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.598
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.067
0.2
157
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
1343
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
239
X-RAY DIFFRACTION
r_nbd_refined
0.214
0.2
179
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.198
0.2
1087
X-RAY DIFFRACTION
r_nbtor_refined
0.155
0.2
580
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.079
0.2
553
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.143
0.2
42
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.148
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.22
0.2
11
X-RAY DIFFRACTION
r_nbd_other
0.236
0.2
46
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.134
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
1.351
1.724
619
X-RAY DIFFRACTION
r_mcbond_other
1.349
1.723
618
X-RAY DIFFRACTION
r_mcangle_it
1.766
2.582
772
X-RAY DIFFRACTION
r_mcangle_other
1.765
2.583
773
X-RAY DIFFRACTION
r_scbond_it
1.885
1.969
579
X-RAY DIFFRACTION
r_scbond_other
1.883
1.97
580
X-RAY DIFFRACTION
r_scangle_it
2.838
2.862
859
X-RAY DIFFRACTION
r_scangle_other
2.837
2.862
860
X-RAY DIFFRACTION
r_lrange_it
5.885
21.132
1188
X-RAY DIFFRACTION
r_lrange_other
5.87
20.916
1184
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.471-1.509
0.453
84
0.467
1112
0.466
2031
0.321
0.223
58.8872
0.464
1.509-1.55
0.422
144
0.383
1647
0.386
2003
0.527
0.568
89.4159
0.375
1.55-1.595
0.369
172
0.341
1778
0.343
1954
0.566
0.612
99.7953
0.325
1.595-1.644
0.317
123
0.316
1781
0.316
1905
0.771
0.764
99.9475
0.301
1.644-1.698
0.344
134
0.288
1722
0.292
1856
0.788
0.806
100
0.264
1.698-1.757
0.296
126
0.264
1641
0.266
1767
0.83
0.855
100
0.232
1.757-1.823
0.251
129
0.241
1592
0.241
1722
0.898
0.897
99.9419
0.204
1.823-1.898
0.253
124
0.22
1538
0.223
1662
0.917
0.928
100
0.187
1.898-1.982
0.262
98
0.212
1482
0.215
1580
0.919
0.931
100
0.176
1.982-2.078
0.213
111
0.201
1429
0.202
1540
0.946
0.948
100
0.171
2.078-2.19
0.218
116
0.207
1330
0.208
1446
0.942
0.941
100
0.18
2.19-2.323
0.307
115
0.217
1291
0.224
1407
0.91
0.932
99.9289
0.192
2.323-2.483
0.246
103
0.221
1211
0.223
1314
0.911
0.933
100
0.2
2.483-2.681
0.256
89
0.235
1123
0.236
1212
0.923
0.931
100
0.219
2.681-2.936
0.24
86
0.227
1055
0.228
1141
0.928
0.933
100
0.228
2.936-3.28
0.251
83
0.224
946
0.226
1029
0.927
0.937
100
0.235
3.28-3.784
0.259
58
0.212
857
0.215
915
0.91
0.946
100
0.242
3.784-4.625
0.198
58
0.177
728
0.179
786
0.962
0.962
100
0.215
4.625-6.503
0.252
60
0.198
578
0.203
638
0.939
0.957
100
0.247
6.503-42.435
0.182
23
0.213
369
0.211
396
0.973
0.96
98.9899
0.257
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
20.6384
-1.4127
13.0893
13.3443
4.1067
27.3752
0.072
0.5859
-0.6629
0.2515
0.1983
-1.4749
0.0736
1.6459
-0.2703
0.2539
0.0233
0.0437
0.2215
0.0195
0.3337
5.2212
27.335
-2.3775
2
5.5315
1.4702
-0.7354
3.8211
0.4205
4.2142
0.029
-0.0583
0.0293
-0.0919
-0.0354
0.1175
0.2319
-0.2103
0.0064
0.2288
-0.0124
-0.0334
0.1409
-0.0129
0.2252
-15.7989
22.817
1.4011
3
28.3693
-4.0309
-4.2376
5.0504
5.1464
9.0224
-0.0214
-0.2004
-0.5966
0.1849
0.1951
-0.2351
0.4281
0.5115
-0.1736
0.3042
-0.0038
0.0093
0.2147
-0.0564
0.235
-3.2158
19.1562
-3.837
4
1.3274
0.1996
-0.5175
0.8509
-0.2851
2.8291
0.1221
-0.0626
-0.1372
-0.0497
-0.1197
-0.0709
0.0596
0.3044
-0.0024
0.1528
-0.0099
-0.0076
0.1436
-0.0014
0.2012
-4.5693
26.5282
7.2618
5
7.0684
2.0885
1.6869
5.3597
0.7725
7.3564
0.2234
0.0661
0.0676
0.0541
-0.0248
0.0799
-0.2232
-0.0792
-0.1985
0.2164
0.0026
0.0581
0.1641
-0.003
0.1978
-13.7609
33.7
14.162
6
2.4633
3.0969
-4.305
3.9101
-5.4552
7.6994
0.5894
-0.2451
0.1942
0.7514
-0.2121
0.2225
-1.1791
0.2037
-0.3773
0.4606
-0.1334
0.1673
0.7472
-0.2652
0.2524
-11.0993
40.4814
24.7947
7
5.1865
-2.2525
-0.1675
8.2238
-0.2501
4.3541
0.2948
-0.0404
0.2315
0.0998
-0.2713
0.1775
-0.6734
0.5175
-0.0235
0.2494
-0.1484
0.052
0.199
-0.0335
0.182
-4.9986
40.5683
15.5848
8
1.9943
-0.8346
0.1021
4.931
0.2362
4.9673
0.2515
-0.1087
-0.2608
0.2505
-0.1255
0.1811
-0.3951
0.515
-0.126
0.213
-0.0929
0.0286
0.2198
-0.0207
0.2013
-4.8178
35.6599
12.1059
9
2.7217
-0.1721
-2.2912
1.8632
-0.6151
9.0215
0.3241
-0.0195
0.1497
0.2194
-0.0333
0.2061
-0.9193
-0.4233
-0.2908
0.2658
-0.0254
0.0576
0.1433
-0.0324
0.2587
-15.6645
38.9103
18.0427
10
16.0908
-9.3143
1.6742
11.238
0.528
6.7049
-0.0434
0.8369
-0.1746
-0.5559
-0.3482
0.124
-0.4962
-0.0023
0.3917
0.2993
-0.0156
0.0059
0.1851
-0.0363
0.244
-2.9336
29.9247
-2.4384
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
ALL
AAA
100 - 105
2
X-RAY DIFFRACTION
2
ALL
AAA
106 - 119
3
X-RAY DIFFRACTION
3
ALL
AAA
120 - 125
4
X-RAY DIFFRACTION
4
ALL
AAA
126 - 174
5
X-RAY DIFFRACTION
5
ALL
AAA
175 - 188
6
X-RAY DIFFRACTION
6
ALL
AAA
189 - 198
7
X-RAY DIFFRACTION
7
ALL
AAA
199 - 210
8
X-RAY DIFFRACTION
8
ALL
AAA
211 - 224
9
X-RAY DIFFRACTION
9
ALL
AAA
225 - 245
10
X-RAY DIFFRACTION
10
ALL
AAA
246 - 254
+
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