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- PDB-4w4m: Crystal structure of PrgK 19-92 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4w4m
TitleCrystal structure of PrgK 19-92
ComponentsLipoprotein PrgK
KeywordsPROTEIN TRANSPORT / T3SS / Salmonella
Function / homology
Function and homology information


protein secretion / cell outer membrane / integral component of membrane
Similarity search - Function
Hypothetical protein rpa1041 / Type III secretion system lipoprotein HrcJ/YscJ / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBergeron, J.R.C. / Strynadka, N.C.J.
CitationJournal: Structure / Year: 2015
Title: The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body.
Authors: Julien R C Bergeron / Liam J Worrall / Soumya De / Nikolaos G Sgourakis / Adrienne H Cheung / Emilie Lameignere / Mark Okon / Gregory A Wasney / David Baker / Lawrence P McIntosh / Natalie C J Strynadka /
Abstract: The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells ...The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells of infected organisms. The molecular details of the assembly of this large, multimembrane-spanning complex remain poorly understood. Here, we report structural, biochemical, and functional analyses of PrgK, an inner-membrane component of the prototypical Salmonella typhimurium T3SS. We have obtained the atomic structures of the two ring building globular domains and show that the C-terminal transmembrane helix is not essential for assembly and secretion. We also demonstrate that structural rearrangement of the two PrgK globular domains, driven by an interconnecting linker region, may promote oligomerization into ring structures. Finally, we used electron microscopy-guided symmetry modeling to propose a structural model for the intimately associated PrgH-PrgK ring interaction within the assembled basal body.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein PrgK
B: Lipoprotein PrgK
C: Lipoprotein PrgK
D: Lipoprotein PrgK
E: Lipoprotein PrgK
F: Lipoprotein PrgK
G: Lipoprotein PrgK
H: Lipoprotein PrgK
I: Lipoprotein PrgK
J: Lipoprotein PrgK
K: Lipoprotein PrgK
L: Lipoprotein PrgK
M: Lipoprotein PrgK
N: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)122,73814
Polymers122,73814
Non-polymers00
Water0
1
A: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)88.120, 112.100, 112.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114B
214C
115B
215D
116B
216E
117B
217F
118B
218G
119B
219H
120B
220I
121B
221J
122B
222K
123B
223L
124B
224M
125B
225N
126C
226D
127C
227E
128C
228F
129C
229G
130C
230H
131C
231I
132C
232J
133C
233K
134C
234L
135C
235M
136C
236N
137D
237E
138D
238F
139D
239G
140D
240H
141D
241I
142D
242J
143D
243K
144D
244L
145D
245M
146D
246N
147E
247F
148E
248G
149E
249H
150E
250I
151E
251J
152E
252K
153E
253L
154E
254M
155E
255N
156F
256G
157F
257H
158F
258I
159F
259J
160F
260K
161F
261L
162F
262M
163F
263N
164G
264H
165G
265I
166G
266J
167G
267K
168G
268L
169G
269M
170G
270N
171H
271I
172H
272J
173H
273K
174H
274L
175H
275M
176H
276N
177I
277J
178I
278K
179I
279L
180I
280M
181I
281N
182J
282K
183J
283L
184J
284M
185J
285N
186K
286L
187K
287M
188K
288N
189L
289M
190L
290N
191M
291N

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A19 - 79
2010B19 - 79
1020A19 - 78
2020C19 - 78
1030A19 - 79
2030D19 - 79
1040A19 - 78
2040E19 - 78
1050A19 - 79
2050F19 - 79
1060A19 - 79
2060G19 - 79
1070A19 - 78
2070H19 - 78
1080A19 - 78
2080I19 - 78
1090A19 - 78
2090J19 - 78
10100A19 - 78
20100K19 - 78
10110A19 - 78
20110L19 - 78
10120A19 - 78
20120M19 - 78
10130A19 - 78
20130N19 - 78
10140B19 - 78
20140C19 - 78
10150B19 - 79
20150D19 - 79
10160B19 - 78
20160E19 - 78
10170B19 - 79
20170F19 - 79
10180B19 - 79
20180G19 - 79
10190B19 - 78
20190H19 - 78
10200B19 - 78
20200I19 - 78
10210B19 - 78
20210J19 - 78
10220B19 - 78
20220K19 - 78
10230B19 - 78
20230L19 - 78
10240B19 - 78
20240M19 - 78
10250B19 - 78
20250N19 - 78
10260C19 - 78
20260D19 - 78
10270C19 - 80
20270E19 - 80
10280C19 - 78
20280F19 - 78
10290C19 - 78
20290G19 - 78
10300C19 - 79
20300H19 - 79
10310C19 - 80
20310I19 - 80
10320C19 - 79
20320J19 - 79
10330C19 - 79
20330K19 - 79
10340C19 - 79
20340L19 - 79
10350C19 - 80
20350M19 - 80
10360C19 - 79
20360N19 - 79
10370D19 - 78
20370E19 - 78
10380D19 - 79
20380F19 - 79
10390D19 - 79
20390G19 - 79
10400D19 - 78
20400H19 - 78
10410D19 - 78
20410I19 - 78
10420D19 - 78
20420J19 - 78
10430D19 - 78
20430K19 - 78
10440D19 - 78
20440L19 - 78
10450D19 - 78
20450M19 - 78
10460D19 - 78
20460N19 - 78
10470E19 - 78
20470F19 - 78
10480E19 - 78
20480G19 - 78
10490E19 - 79
20490H19 - 79
10500E19 - 80
20500I19 - 80
10510E19 - 79
20510J19 - 79
10520E19 - 79
20520K19 - 79
10530E19 - 79
20530L19 - 79
10540E19 - 80
20540M19 - 80
10550E19 - 79
20550N19 - 79
10560F19 - 79
20560G19 - 79
10570F19 - 78
20570H19 - 78
10580F19 - 78
20580I19 - 78
10590F19 - 78
20590J19 - 78
10600F19 - 78
20600K19 - 78
10610F19 - 78
20610L19 - 78
10620F19 - 78
20620M19 - 78
10630F19 - 78
20630N19 - 78
10640G19 - 78
20640H19 - 78
10650G19 - 78
20650I19 - 78
10660G19 - 78
20660J19 - 78
10670G19 - 78
20670K19 - 78
10680G19 - 78
20680L19 - 78
10690G19 - 78
20690M19 - 78
10700G19 - 78
20700N19 - 78
10710H19 - 79
20710I19 - 79
10720H19 - 82
20720J19 - 82
10730H19 - 82
20730K19 - 82
10740H19 - 82
20740L19 - 82
10750H19 - 79
20750M19 - 79
10760H19 - 80
20760N19 - 80
10770I19 - 79
20770J19 - 79
10780I19 - 79
20780K19 - 79
10790I19 - 79
20790L19 - 79
10800I19 - 80
20800M19 - 80
10810I19 - 79
20810N19 - 79
10820J19 - 82
20820K19 - 82
10830J19 - 82
20830L19 - 82
10840J19 - 79
20840M19 - 79
10850J19 - 80
20850N19 - 80
10860K19 - 82
20860L19 - 82
10870K19 - 79
20870M19 - 79
10880K19 - 80
20880N19 - 80
10890L19 - 79
20890M19 - 79
10900L19 - 80
20900N19 - 80
10910M19 - 79
20910N19 - 79

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91

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Components

#1: Protein
Lipoprotein PrgK


Mass: 8766.982 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: prgK, STM2871 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P41786

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 80 mM Phosphate buffer pH 4.0, 20 mM Tris pH 7.0, 25 % PEG 300, 20 mM MgCl2, 20 mM NaCl

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9511 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9511 Å / Relative weight: 1
ReflectionResolution: 3.2→79.39 Å / Num. obs: 17949 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 4.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→79.39 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.839 / SU B: 26.997 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27951 975 5.2 %RANDOM
Rwork0.24612 ---
obs0.24783 17949 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.833 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å20 Å20 Å2
2---3.85 Å20 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 3.2→79.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 0 0 6912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027043
X-RAY DIFFRACTIONr_bond_other_d0.0090.026882
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9729552
X-RAY DIFFRACTIONr_angle_other_deg1.996315910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.4715858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36426.573321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.884151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6741513
X-RAY DIFFRACTIONr_chiral_restr0.0960.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217868
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021437
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35760.1
12B35760.1
21A35020.12
22C35020.12
31A35960.09
32D35960.09
41A35200.1
42E35200.1
51A35450.11
52F35450.11
61A35440.11
62G35440.11
71A35760.08
72H35760.08
81A35310.1
82I35310.1
91A35590.09
92J35590.09
101A35160.1
102K35160.1
111A34850.11
112L34850.11
121A32170.14
122M32170.14
131A35020.11
132N35020.11
141B35670.12
142C35670.12
151B35740.1
152D35740.1
161B35150.1
162E35150.1
171B36190.1
172F36190.1
181B36500.1
182G36500.1
191B35540.11
192H35540.11
201B35070.12
202I35070.12
211B35570.11
212J35570.11
221B36110.09
222K36110.09
231B35420.11
232L35420.11
241B32970.14
242M32970.14
251B35220.11
252N35220.11
261C34920.11
262D34920.11
271C36220.12
272E36220.12
281C35540.11
282F35540.11
291C35390.12
292G35390.12
301C36310.11
302H36310.11
311C36380.13
312I36380.13
321C35970.12
322J35970.12
331C36400.11
332K36400.11
341C36110.11
342L36110.11
351C34230.14
352M34230.14
361C35620.13
362N35620.13
371D35450.08
372E35450.08
381D35580.1
382F35580.1
391D35460.1
392G35460.1
401D35920.07
402H35920.07
411D35890.09
412I35890.09
421D35630.09
422J35630.09
431D35010.1
432K35010.1
441D35000.09
442L35000.09
451D32120.14
452M32120.14
461D35130.1
462N35130.1
471E34940.1
472F34940.1
481E35120.09
482G35120.09
491E36490.08
492H36490.08
501E36650.11
502I36650.11
511E36120.11
512J36120.11
521E35780.1
522K35780.1
531E35560.11
532L35560.11
541E33560.14
542M33560.14
551E36020.1
552N36020.1
561F36750.07
562G36750.07
571F35290.1
572H35290.1
581F35060.11
582I35060.11
591F35110.12
592J35110.12
601F35810.08
602K35810.08
611F35070.11
612L35070.11
621F32610.14
622M32610.14
631F34650.12
632N34650.12
641G35250.1
642H35250.1
651G35010.11
652I35010.11
661G35210.11
662J35210.11
671G35870.09
672K35870.09
681G35160.11
682L35160.11
691G32720.14
692M32720.14
701G34690.12
702N34690.12
711H36620.08
712I36620.08
721H38320.1
722J38320.1
731H37720.1
732K37720.1
741H37370.11
742L37370.11
751H33510.13
752M33510.13
761H37100.1
762N37100.1
771I36620.09
772J36620.09
781I35880.11
782K35880.11
791I36050.09
792L36050.09
801I33550.14
802M33550.14
811I36160.1
812N36160.1
821J38080.11
822K38080.11
831J37480.11
832L37480.11
841J33690.13
842M33690.13
851J37060.1
852N37060.1
861K37740.11
862L37740.11
871K34060.12
872M34060.12
881K36360.11
882N36360.11
891L33740.13
892M33740.13
901L36010.12
902N36010.12
911M33030.14
912N33030.14
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 80 -
Rwork0.318 1285 -
obs--100 %

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  • 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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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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

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