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- PDB-6rjh: 3D structure of horse spleen apoferritin determined using multifu... -

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Basic information

Entry
Database: PDB / ID: 6rjh
Title3D structure of horse spleen apoferritin determined using multifunctional graphene supports for electron cryomicroscopy
ComponentsFerritin light chain
KeywordsMETAL TRANSPORT
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsNaydenova, K. / Peet, M.J. / Russo, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/17 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Multifunctional graphene supports for electron cryomicroscopy.
Authors: Katerina Naydenova / Mathew J Peet / Christopher J Russo /
Abstract: With recent technological advances, the atomic resolution structure of any purified biomolecular complex can, in principle, be determined by single-particle electron cryomicroscopy (cryoEM). In ...With recent technological advances, the atomic resolution structure of any purified biomolecular complex can, in principle, be determined by single-particle electron cryomicroscopy (cryoEM). In practice, the primary barrier to structure determination is the preparation of a frozen specimen suitable for high-resolution imaging. To address this, we present a multifunctional specimen support for cryoEM, comprising large-crystal monolayer graphene suspended across the surface of an ultrastable gold specimen support. Using a low-energy plasma surface modification system, we tune the surface of this support to the specimen by patterning a range of covalent functionalizations across the graphene layer on a single grid. This support design reduces specimen movement during imaging, improves image quality, and allows high-resolution structure determination with a minimum of material and data.
History
DepositionApr 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Category: em_admin / pdbx_database_proc / Item: _em_admin.last_update
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 1.3Dec 18, 2019Group: Data collection / Other / Category: atom_sites / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Ferritin light chain
B: Ferritin light chain
C: Ferritin light chain
D: Ferritin light chain
E: Ferritin light chain
F: Ferritin light chain
G: Ferritin light chain
H: Ferritin light chain
I: Ferritin light chain
J: Ferritin light chain
K: Ferritin light chain
L: Ferritin light chain
M: Ferritin light chain
N: Ferritin light chain
O: Ferritin light chain
P: Ferritin light chain
Q: Ferritin light chain
R: Ferritin light chain
S: Ferritin light chain
T: Ferritin light chain
U: Ferritin light chain
V: Ferritin light chain
W: Ferritin light chain
X: Ferritin light chain


Theoretical massNumber of molelcules
Total (without water)468,77124
Polymers468,77124
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
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
114A
214O
115A
215P
116A
216Q
117A
217R
118A
218S
119A
219T
120A
220U
121A
221V
122A
222W
123A
223X
124B
224C
125B
225D
126B
226E
127B
227F
128B
228G
129B
229H
130B
230I
131B
231J
132B
232K
133B
233L
134B
234M
135B
235N
136B
236O
137B
237P
138B
238Q
139B
239R
140B
240S
141B
241T
142B
242U
143B
243V
144B
244W
145B
245X
146C
246D
147C
247E
148C
248F
149C
249G
150C
250H
151C
251I
152C
252J
153C
253K
154C
254L
155C
255M
156C
256N
157C
257O
158C
258P
159C
259Q
160C
260R
161C
261S
162C
262T
163C
263U
164C
264V
165C
265W
166C
266X
167D
267E
168D
268F
169D
269G
170D
270H
171D
271I
172D
272J
173D
273K
174D
274L
175D
275M
176D
276N
177D
277O
178D
278P
179D
279Q
180D
280R
181D
281S
182D
282T
183D
283U
184D
284V
185D
285W
186D
286X
187E
287F
188E
288G
189E
289H
190E
290I
191E
291J
192E
292K
193E
293L
194E
294M
195E
295N
196E
296O
197E
297P
198E
298Q
199E
299R
1100E
2100S
1101E
2101T
1102E
2102U
1103E
2103V
1104E
2104W
1105E
2105X
1106F
2106G
1107F
2107H
1108F
2108I
1109F
2109J
1110F
2110K
1111F
2111L
1112F
2112M
1113F
2113N
1114F
2114O
1115F
2115P
1116F
2116Q
1117F
2117R
1118F
2118S
1119F
2119T
1120F
2120U
1121F
2121V
1122F
2122W
1123F
2123X
1124G
2124H
1125G
2125I
1126G
2126J
1127G
2127K
1128G
2128L
1129G
2129M
1130G
2130N
1131G
2131O
1132G
2132P
1133G
2133Q
1134G
2134R
1135G
2135S
1136G
2136T
1137G
2137U
1138G
2138V
1139G
2139W
1140G
2140X
1141H
2141I
1142H
2142J
1143H
2143K
1144H
2144L
1145H
2145M
1146H
2146N
1147H
2147O
1148H
2148P
1149H
2149Q
1150H
2150R
1151H
2151S
1152H
2152T
1153H
2153U
1154H
2154V
1155H
2155W
1156H
2156X
1157I
2157J
1158I
2158K
1159I
2159L
1160I
2160M
1161I
2161N
1162I
2162O
1163I
2163P
1164I
2164Q
1165I
2165R
1166I
2166S
1167I
2167T
1168I
2168U
1169I
2169V
1170I
2170W
1171I
2171X
1172J
2172K
1173J
2173L
1174J
2174M
1175J
2175N
1176J
2176O
1177J
2177P
1178J
2178Q
1179J
2179R
1180J
2180S
1181J
2181T
1182J
2182U
1183J
2183V
1184J
2184W
1185J
2185X
1186K
2186L
1187K
2187M
1188K
2188N
1189K
2189O
1190K
2190P
1191K
2191Q
1192K
2192R
1193K
2193S
1194K
2194T
1195K
2195U
1196K
2196V
1197K
2197W
1198K
2198X
1199L
2199M
1200L
2200N
1201L
2201O
1202L
2202P
1203L
2203Q
1204L
2204R
1205L
2205S
1206L
2206T
1207L
2207U
1208L
2208V
1209L
2209W
1210L
2210X
1211M
2211N
1212M
2212O
1213M
2213P
1214M
2214Q
1215M
2215R
1216M
2216S
1217M
2217T
1218M
2218U
1219M
2219V
1220M
2220W
1221M
2221X
1222N
2222O
1223N
2223P
1224N
2224Q
1225N
2225R
1226N
2226S
1227N
2227T
1228N
2228U
1229N
2229V
1230N
2230W
1231N
2231X
1232O
2232P
1233O
2233Q
1234O
2234R
1235O
2235S
1236O
2236T
1237O
2237U
1238O
2238V
1239O
2239W
1240O
2240X
1241P
2241Q
1242P
2242R
1243P
2243S
1244P
2244T
1245P
2245U
1246P
2246V
1247P
2247W
1248P
2248X
1249Q
2249R
1250Q
2250S
1251Q
2251T
1252Q
2252U
1253Q
2253V
1254Q
2254W
1255Q
2255X
1256R
2256S
1257R
2257T
1258R
2258U
1259R
2259V
1260R
2260W
1261R
2261X
1262S
2262T
1263S
2263U
1264S
2264V
1265S
2265W
1266S
2266X
1267T
2267U
1268T
2268V
1269T
2269W
1270T
2270X
1271U
2271V
1272U
2272W
1273U
2273X
1274V
2274W
1275V
2275X
1276W
2276X

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 171
2111B2 - 171
1121A2 - 171
2121C2 - 171
1131A2 - 171
2131D2 - 171
1141A2 - 171
2141E2 - 171
1151A2 - 171
2151F2 - 171
1161A2 - 171
2161G2 - 171
1171A2 - 171
2171H2 - 171
1181A2 - 171
2181I2 - 171
1191A2 - 171
2191J2 - 171
11101A2 - 171
21101K2 - 171
11111A2 - 171
21111L2 - 171
11121A2 - 171
21121M2 - 171
11131A2 - 171
21131N2 - 171
11141A2 - 171
21141O2 - 171
11151A2 - 171
21151P2 - 171
11161A2 - 171
21161Q2 - 171
11171A2 - 171
21171R2 - 171
11181A2 - 171
21181S2 - 171
11191A2 - 171
21191T2 - 171
11201A2 - 171
21201U2 - 171
11211A2 - 171
21211V2 - 171
11221A2 - 171
21221W2 - 171
11231A2 - 171
21231X2 - 171
11241B2 - 171
21241C2 - 171
11251B2 - 171
21251D2 - 171
11261B2 - 171
21261E2 - 171
11271B2 - 171
21271F2 - 171
11281B2 - 171
21281G2 - 171
11291B2 - 171
21291H2 - 171
11301B2 - 171
21301I2 - 171
11311B2 - 171
21311J2 - 171
11321B2 - 171
21321K2 - 171
11331B2 - 171
21331L2 - 171
11341B2 - 171
21341M2 - 171
11351B2 - 171
21351N2 - 171
11361B2 - 171
21361O2 - 171
11371B2 - 171
21371P2 - 171
11381B2 - 171
21381Q2 - 171
11391B2 - 171
21391R2 - 171
11401B2 - 171
21401S2 - 171
11411B2 - 171
21411T2 - 171
11421B2 - 171
21421U2 - 171
11431B2 - 171
21431V2 - 171
11441B2 - 171
21441W2 - 171
11451B2 - 171
21451X2 - 171
11461C2 - 171
21461D2 - 171
11471C2 - 171
21471E2 - 171
11481C2 - 171
21481F2 - 171
11491C2 - 171
21491G2 - 171
11501C2 - 171
21501H2 - 171
11511C2 - 171
21511I2 - 171
11521C2 - 171
21521J2 - 171
11531C2 - 171
21531K2 - 171
11541C2 - 171
21541L2 - 171
11551C2 - 171
21551M2 - 171
11561C2 - 171
21561N2 - 171
11571C2 - 171
21571O2 - 171
11581C2 - 171
21581P2 - 171
11591C2 - 171
21591Q2 - 171
11601C2 - 171
21601R2 - 171
11611C2 - 171
21611S2 - 171
11621C2 - 171
21621T2 - 171
11631C2 - 171
21631U2 - 171
11641C2 - 171
21641V2 - 171
11651C2 - 171
21651W2 - 171
11661C2 - 171
21661X2 - 171
11671D2 - 171
21671E2 - 171
11681D2 - 171
21681F2 - 171
11691D2 - 171
21691G2 - 171
11701D2 - 171
21701H2 - 171
11711D2 - 171
21711I2 - 171
11721D2 - 171
21721J2 - 171
11731D2 - 171
21731K2 - 171
11741D2 - 171
21741L2 - 171
11751D2 - 171
21751M2 - 171
11761D2 - 171
21761N2 - 171
11771D2 - 171
21771O2 - 171
11781D2 - 171
21781P2 - 171
11791D2 - 171
21791Q2 - 171
11801D2 - 171
21801R2 - 171
11811D2 - 171
21811S2 - 171
11821D2 - 171
21821T2 - 171
11831D2 - 171
21831U2 - 171
11841D2 - 171
21841V2 - 171
11851D2 - 171
21851W2 - 171
11861D2 - 171
21861X2 - 171
11871E2 - 171
21871F2 - 171
11881E2 - 171
21881G2 - 171
11891E2 - 171
21891H2 - 171
11901E2 - 171
21901I2 - 171
11911E2 - 171
21911J2 - 171
11921E2 - 171
21921K2 - 171
11931E2 - 171
21931L2 - 171
11941E2 - 171
21941M2 - 171
11951E2 - 171
21951N2 - 171
11961E2 - 171
21961O2 - 171
11971E2 - 171
21971P2 - 171
11981E2 - 171
21981Q2 - 171
11991E2 - 171
21991R2 - 171
111001E2 - 171
211001S2 - 171
111011E2 - 171
211011T2 - 171
111021E2 - 171
211021U2 - 171
111031E2 - 171
211031V2 - 171
111041E2 - 171
211041W2 - 171
111051E2 - 171
211051X2 - 171
111061F2 - 171
211061G2 - 171
111071F2 - 171
211071H2 - 171
111081F2 - 171
211081I2 - 171
111091F2 - 171
211091J2 - 171
111101F2 - 171
211101K2 - 171
111111F2 - 171
211111L2 - 171
111121F2 - 171
211121M2 - 171
111131F2 - 171
211131N2 - 171
111141F2 - 171
211141O2 - 171
111151F2 - 171
211151P2 - 171
111161F2 - 171
211161Q2 - 171
111171F2 - 171
211171R2 - 171
111181F2 - 171
211181S2 - 171
111191F2 - 171
211191T2 - 171
111201F2 - 171
211201U2 - 171
111211F2 - 171
211211V2 - 171
111221F2 - 171
211221W2 - 171
111231F2 - 171
211231X2 - 171
111241G2 - 171
211241H2 - 171
111251G2 - 171
211251I2 - 171
111261G2 - 171
211261J2 - 171
111271G2 - 171
211271K2 - 171
111281G2 - 171
211281L2 - 171
111291G2 - 171
211291M2 - 171
111301G2 - 171
211301N2 - 171
111311G2 - 171
211311O2 - 171
111321G2 - 171
211321P2 - 171
111331G2 - 171
211331Q2 - 171
111341G2 - 171
211341R2 - 171
111351G2 - 171
211351S2 - 171
111361G2 - 171
211361T2 - 171
111371G2 - 171
211371U2 - 171
111381G2 - 171
211381V2 - 171
111391G2 - 171
211391W2 - 171
111401G2 - 171
211401X2 - 171
111411H2 - 171
211411I2 - 171
111421H2 - 171
211421J2 - 171
111431H2 - 171
211431K2 - 171
111441H2 - 171
211441L2 - 171
111451H2 - 171
211451M2 - 171
111461H2 - 171
211461N2 - 171
111471H2 - 171
211471O2 - 171
111481H2 - 171
211481P2 - 171
111491H2 - 171
211491Q2 - 171
111501H2 - 171
211501R2 - 171
111511H2 - 171
211511S2 - 171
111521H2 - 171
211521T2 - 171
111531H2 - 171
211531U2 - 171
111541H2 - 171
211541V2 - 171
111551H2 - 171
211551W2 - 171
111561H2 - 171
211561X2 - 171
111571I2 - 171
211571J2 - 171
111581I2 - 171
211581K2 - 171
111591I2 - 171
211591L2 - 171
111601I2 - 171
211601M2 - 171
111611I2 - 171
211611N2 - 171
111621I2 - 171
211621O2 - 171
111631I2 - 171
211631P2 - 171
111641I2 - 171
211641Q2 - 171
111651I2 - 171
211651R2 - 171
111661I2 - 171
211661S2 - 171
111671I2 - 171
211671T2 - 171
111681I2 - 171
211681U2 - 171
111691I2 - 171
211691V2 - 171
111701I2 - 171
211701W2 - 171
111711I2 - 171
211711X2 - 171
111721J2 - 171
211721K2 - 171
111731J2 - 171
211731L2 - 171
111741J2 - 171
211741M2 - 171
111751J2 - 171
211751N2 - 171
111761J2 - 171
211761O2 - 171
111771J2 - 171
211771P2 - 171
111781J2 - 171
211781Q2 - 171
111791J2 - 171
211791R2 - 171
111801J2 - 171
211801S2 - 171
111811J2 - 171
211811T2 - 171
111821J2 - 171
211821U2 - 171
111831J2 - 171
211831V2 - 171
111841J2 - 171
211841W2 - 171
111851J2 - 171
211851X2 - 171
111861K2 - 171
211861L2 - 171
111871K2 - 171
211871M2 - 171
111881K2 - 171
211881N2 - 171
111891K2 - 171
211891O2 - 171
111901K2 - 171
211901P2 - 171
111911K2 - 171
211911Q2 - 171
111921K2 - 171
211921R2 - 171
111931K2 - 171
211931S2 - 171
111941K2 - 171
211941T2 - 171
111951K2 - 171
211951U2 - 171
111961K2 - 171
211961V2 - 171
111971K2 - 171
211971W2 - 171
111981K2 - 171
211981X2 - 171
111991L2 - 171
211991M2 - 171
112001L2 - 171
212001N2 - 171
112011L2 - 171
212011O2 - 171
112021L2 - 171
212021P2 - 171
112031L2 - 171
212031Q2 - 171
112041L2 - 171
212041R2 - 171
112051L2 - 171
212051S2 - 171
112061L2 - 171
212061T2 - 171
112071L2 - 171
212071U2 - 171
112081L2 - 171
212081V2 - 171
112091L2 - 171
212091W2 - 171
112101L2 - 171
212101X2 - 171
112111M2 - 171
212111N2 - 171
112121M2 - 171
212121O2 - 171
112131M2 - 171
212131P2 - 171
112141M2 - 171
212141Q2 - 171
112151M2 - 171
212151R2 - 171
112161M2 - 171
212161S2 - 171
112171M2 - 171
212171T2 - 171
112181M2 - 171
212181U2 - 171
112191M2 - 171
212191V2 - 171
112201M2 - 171
212201W2 - 171
112211M2 - 171
212211X2 - 171
112221N2 - 171
212221O2 - 171
112231N2 - 171
212231P2 - 171
112241N2 - 171
212241Q2 - 171
112251N2 - 171
212251R2 - 171
112261N2 - 171
212261S2 - 171
112271N2 - 171
212271T2 - 171
112281N2 - 171
212281U2 - 171
112291N2 - 171
212291V2 - 171
112301N2 - 171
212301W2 - 171
112311N2 - 171
212311X2 - 171
112321O2 - 171
212321P2 - 171
112331O2 - 171
212331Q2 - 171
112341O2 - 171
212341R2 - 171
112351O2 - 171
212351S2 - 171
112361O2 - 171
212361T2 - 171
112371O2 - 171
212371U2 - 171
112381O2 - 171
212381V2 - 171
112391O2 - 171
212391W2 - 171
112401O2 - 171
212401X2 - 171
112411P2 - 171
212411Q2 - 171
112421P2 - 171
212421R2 - 171
112431P2 - 171
212431S2 - 171
112441P2 - 171
212441T2 - 171
112451P2 - 171
212451U2 - 171
112461P2 - 171
212461V2 - 171
112471P2 - 171
212471W2 - 171
112481P2 - 171
212481X2 - 171
112491Q2 - 171
212491R2 - 171
112501Q2 - 171
212501S2 - 171
112511Q2 - 171
212511T2 - 171
112521Q2 - 171
212521U2 - 171
112531Q2 - 171
212531V2 - 171
112541Q2 - 171
212541W2 - 171
112551Q2 - 171
212551X2 - 171
112561R2 - 171
212561S2 - 171
112571R2 - 171
212571T2 - 171
112581R2 - 171
212581U2 - 171
112591R2 - 171
212591V2 - 171
112601R2 - 171
212601W2 - 171
112611R2 - 171
212611X2 - 171
112621S2 - 171
212621T2 - 171
112631S2 - 171
212631U2 - 171
112641S2 - 171
212641V2 - 171
112651S2 - 171
212651W2 - 171
112661S2 - 171
212661X2 - 171
112671T2 - 171
212671U2 - 171
112681T2 - 171
212681V2 - 171
112691T2 - 171
212691W2 - 171
112701T2 - 171
212701X2 - 171
112711U2 - 171
212711V2 - 171
112721U2 - 171
212721W2 - 171
112731U2 - 171
212731X2 - 171
112741V2 - 171
212741W2 - 171
112751V2 - 171
212751X2 - 171
112761W2 - 171
212761X2 - 171

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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(1, 2.4E-5, -8.0E-6), (8.0E-6, 3.2E-5, 1), (2.4E-5, -1, 3.2E-5)-0.00014, -0.00474, 220.82561

-
Components

#1: Protein ...
Ferritin light chain / / Ferritin L subunit


Mass: 19532.113 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: ApoferritinFerritin / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Equus caballus (horse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Homemade
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 37 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

SoftwareName: REFMAC / Version: 5.8.0231 / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
12RELION3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41202 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4V1W
RefinementResolution: 2→220.83 Å / Cor.coef. Fo:Fc: 0.829 / SU B: 1.588 / SU ML: 0.037 / ESU R: 0.077
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.3484 --
obs0.3484 2820029 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.175 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→220.83 Å / Total: 32736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0370.01233264
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg5.5661.62744784
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.39454056
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.46922.4712040
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.604156048
ELECTRON MICROSCOPYr_dihedral_angle_4_deg23.54315264
ELECTRON MICROSCOPYr_chiral_restr0.3250.24056
ELECTRON MICROSCOPYr_gen_planes_refined0.0330.0225584
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.7242.11416296
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it10.5143.23420328
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it15.1173.18416968
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined20.65744.748151159
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Number: 1364 / Refine-ID: ELECTRON MICROSCOPY

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1010Atight positional0.010.24
1111Atight positional0.010.24
1212Atight positional0.010.24
1313Atight positional0.030.24
1414Atight positional0.030.24
1515Atight positional0.010.24
1616Atight positional0.030.24
1717Atight positional0.010.24
1818Atight positional0.010.24
1919Atight positional0.010.24
2020Atight positional0.010.24
2121Atight positional0.030.24
2222Atight positional0.010.24
2323Atight positional0.010.24
2424Atight positional00.24
2525Atight positional0.030.24
2626Atight positional0.010.24
2727Atight positional0.010.24
2828Atight positional00.24
2929Atight positional00.24
3030Atight positional0.010.24
3131Atight positional0.010.24
3232Atight positional0.010.24
3333Atight positional00.24
3434Atight positional0.010.24
3535Atight positional0.030.24
3636Atight positional0.030.24
3737Atight positional0.010.24
3838Atight positional0.030.24
3939Atight positional00.24
4040Atight positional00.24
4141Atight positional00.24
4242Atight positional00.24
4343Atight positional0.030.24
4444Atight positional00.24
4545Atight positional0.010.24
4646Atight positional0.030.24
4747Atight positional0.010.24
4848Atight positional0.010.24
4949Atight positional00.24
5050Atight positional00.24
5151Atight positional0.010.24
5252Atight positional0.010.24
5353Atight positional00.24
5454Atight positional00.24
5555Atight positional0.010.24
5656Atight positional0.030.24
5757Atight positional0.030.24
5858Atight positional0.010.24
5959Atight positional0.030.24
6060Atight positional00.24
6161Atight positional00.24
6262Atight positional00.24
6363Atight positional00.24
6464Atight positional0.030.24
6565Atight positional00.24
6666Atight positional00.24
6767Atight positional0.030.24
6868Atight positional0.030.24
6969Atight positional0.030.24
7070Atight positional0.030.24
7171Atight positional0.030.24
7272Atight positional0.030.24
7373Atight positional0.030.24
7474Atight positional0.030.24
7575Atight positional0.030.24
7676Atight positional00.24
7777Atight positional00.24
7878Atight positional0.030.24
7979Atight positional00.24
8080Atight positional0.030.24
8181Atight positional0.030.24
8282Atight positional0.030.24
8383Atight positional0.030.24
8484Atight positional00.24
8585Atight positional0.030.24
8686Atight positional0.030.24
8787Atight positional00.24
8888Atight positional00.24
8989Atight positional0.010.24
9090Atight positional0.010.24
9191Atight positional00.24
9292Atight positional00.24
9393Atight positional00.24
9494Atight positional00.24
9595Atight positional0.020.24
9696Atight positional0.030.24
9797Atight positional00.24
9898Atight positional0.030.24
9999Atight positional00.24
100100Atight positional0.010.24
101101Atight positional00.24
102102Atight positional00.24
103103Atight positional0.030.24
104104Atight positional00.24
105105Atight positional00.24
106106Atight positional00.24
107107Atight positional0.010.24
108108Atight positional0.010.24
109109Atight positional00.24
110110Atight positional00.24
111111Atight positional00.24
112112Atight positional00.24
113113Atight positional0.020.24
114114Atight positional0.030.24
115115Atight positional00.24
116116Atight positional0.030.24
117117Atight positional00.24
118118Atight positional0.010.24
119119Atight positional00.24
120120Atight positional0.010.24
121121Atight positional0.030.24
122122Atight positional00.24
123123Atight positional00.24
124124Atight positional00.24
125125Atight positional00.24
126126Atight positional00.24
127127Atight positional00.24
128128Atight positional00.24
129129Atight positional00.24
130130Atight positional0.020.24
131131Atight positional0.030.24
132132Atight positional00.24
133133Atight positional0.030.24
134134Atight positional00.24
135135Atight positional00.24
136136Atight positional00.24
137137Atight positional00.24
138138Atight positional0.030.24
139139Atight positional00.24
140140Atight positional00.24
141141Atight positional0.010.24
142142Atight positional0.010.24
143143Atight positional0.010.24
144144Atight positional00.24
145145Atight positional0.010.24
146146Atight positional0.030.24
147147Atight positional0.030.24
148148Atight positional0.010.24
149149Atight positional0.030.24
150150Atight positional00.24
151151Atight positional00.24
152152Atight positional00.24
153153Atight positional00.24
154154Atight positional0.030.24
155155Atight positional0.010.24
156156Atight positional00.24
157157Atight positional00.24
158158Atight positional0.010.24
159159Atight positional00.24
160160Atight positional00.24
161161Atight positional0.030.24
162162Atight positional0.030.24
163163Atight positional00.24
164164Atight positional0.030.24
165165Atight positional0.010.24
166166Atight positional0.010.24
167167Atight positional0.010.24
168168Atight positional0.010.24
169169Atight positional0.030.24
170170Atight positional0.010.24
171171Atight positional0.010.24
172172Atight positional00.24
173173Atight positional00.24
174174Atight positional00.24
175175Atight positional0.020.24
176176Atight positional0.030.24
177177Atight positional00.24
178178Atight positional0.030.24
179179Atight positional00.24
180180Atight positional00.24
181181Atight positional0.010.24
182182Atight positional00.24
183183Atight positional0.030.24
184184Atight positional00.24
185185Atight positional00.24
186186Atight positional00.24
187187Atight positional00.24
188188Atight positional0.020.24
189189Atight positional0.030.24
190190Atight positional00.24
191191Atight positional0.030.24
192192Atight positional00.24
193193Atight positional00.24
194194Atight positional00.24
195195Atight positional00.24
196196Atight positional0.030.24
197197Atight positional00.24
198198Atight positional00.24
199199Atight positional00.24
200200Atight positional0.020.24
201201Atight positional0.030.24
202202Atight positional00.24
203203Atight positional0.030.24
204204Atight positional00.24
205205Atight positional00.24
206206Atight positional00.24
207207Atight positional00.24
208208Atight positional0.030.24
209209Atight positional00.24
210210Atight positional00.24
211211Atight positional0.020.24
212212Atight positional0.030.24
213213Atight positional00.24
214214Atight positional0.030.24
215215Atight positional00.24
216216Atight positional0.010.24
217217Atight positional0.010.24
218218Atight positional00.24
219219Atight positional0.030.24
220220Atight positional00.24
221221Atight positional00.24
222222Atight positional0.010.24
223223Atight positional0.020.24
224224Atight positional0.010.24
225225Atight positional0.030.24
226226Atight positional0.030.24
227227Atight positional0.020.24
228228Atight positional0.030.24
229229Atight positional00.24
230230Atight positional0.020.24
231231Atight positional0.020.24
232232Atight positional0.030.24
233233Atight positional00.24
234234Atight positional0.030.24
235235Atight positional0.030.24
236236Atight positional0.030.24
237237Atight positional0.030.24
238238Atight positional00.24
239239Atight positional0.030.24
240240Btight positional0.030.24
241241Btight positional0.030.24
242242Btight positional00.24
243243Btight positional00.24
244244Btight positional0.010.24
245245Btight positional00.24
246246Btight positional0.030.24
247247Btight positional00.24
248248Btight positional00.24
249249Btight positional0.030.24
250250Btight positional0.030.24
251251Btight positional0.030.24
252252Btight positional0.030.24
253253Btight positional00.24
254254Btight positional0.030.24
255255Btight positional0.030.24
256256Btight positional00.24
257257Btight positional00.24
258258Btight positional00.24
259259Btight positional0.030.24
260260Btight positional00.24
261261Btight positional00.24
262262Btight positional00.24
263263Btight positional00.24
264264Btight positional0.030.24
265265Btight positional00.24
266266Btight positional00.24
267267Btight positional00.24
268268Btight positional0.030.24
269269Btight positional00.24
270270Btight positional00.24
271271Btight positional0.030.24
272272Btight positional00.24
273273Btight positional00.24
274274Btight positional0.030.24
275275Btight positional0.030.24
276276Btight positional00.24
11Atight thermal0.282.4
22Atight thermal0.252.4
33Atight thermal1.082.4
44Atight thermal0.312.4
55Atight thermal0.32.4
66Atight thermal0.292.4
77Atight thermal0.282.4
88Atight thermal0.362.4
99Atight thermal0.322.4
1010Atight thermal0.282.4
1111Atight thermal0.32.4
1212Atight thermal0.292.4
1313Atight thermal12.4
1414Atight thermal1.072.4
1515Atight thermal0.32.4
1616Atight thermal1.072.4
1717Atight thermal0.272.4
1818Atight thermal0.282.4
1919Atight thermal0.252.4
2020Atight thermal0.282.4
2121Atight thermal1.072.4
2222Atight thermal0.312.4
2323Atight thermal0.282.4
2424Btight thermal0.112.4
2525Btight thermal1.072.4
2626Btight thermal0.162.4
2727Btight thermal0.192.4
2828Btight thermal0.152.4
2929Btight thermal0.122.4
3030Btight thermal0.252.4
3131Btight thermal0.172.4
3232Btight thermal0.162.4
3333Btight thermal0.162.4
3434Btight thermal0.152.4
3535Btight thermal0.992.4
3636Btight thermal1.072.4
3737Btight thermal0.162.4
3838Btight thermal1.062.4
3939Btight thermal0.12.4
4040Btight thermal0.12.4
4141Btight thermal0.132.4
4242Btight thermal0.072.4
4343Btight thermal1.062.4
4444Btight thermal0.152.4
4545Btight thermal0.162.4
4646Ctight thermal1.072.4
4747Ctight thermal0.162.4
4848Ctight thermal0.182.4
4949Ctight thermal0.142.4
5050Ctight thermal0.122.4
5151Ctight thermal0.262.4
5252Ctight thermal0.192.4
5353Ctight thermal0.132.4
5454Ctight thermal0.162.4
5555Ctight thermal0.142.4
5656Ctight thermal0.992.4
5757Ctight thermal1.062.4
5858Ctight thermal0.162.4
5959Ctight thermal1.062.4
6060Ctight thermal0.082.4
6161Ctight thermal0.112.4
6262Ctight thermal0.12.4
6363Ctight thermal0.12.4
6464Ctight thermal1.062.4
6565Ctight thermal0.152.4
6666Ctight thermal0.142.4
6767Dtight thermal1.062.4
6868Dtight thermal1.052.4
6969Dtight thermal1.072.4
7070Dtight thermal1.082.4
7171Dtight thermal1.072.4
7272Dtight thermal1.062.4
7373Dtight thermal1.072.4
7474Dtight thermal1.072.4
7575Dtight thermal1.072.4
7676Dtight thermal0.122.4
7777Dtight thermal0.082.4
7878Dtight thermal1.062.4
7979Dtight thermal0.092.4
8080Dtight thermal1.072.4
8181Dtight thermal1.082.4
8282Dtight thermal1.072.4
8383Dtight thermal1.082.4
8484Dtight thermal0.092.4
8585Dtight thermal1.072.4
8686Dtight thermal1.072.4
8787Etight thermal0.122.4
8888Etight thermal0.092.4
8989Etight thermal0.172.4
9090Etight thermal0.182.4
9191Etight thermal0.122.4
9292Etight thermal0.112.4
9393Etight thermal0.12.4
9494Etight thermal0.072.4
9595Etight thermal0.982.4
9696Etight thermal1.052.4
9797Etight thermal0.072.4
9898Etight thermal1.052.4
9999Etight thermal0.162.4
100100Etight thermal0.162.4
101101Etight thermal0.172.4
102102Etight thermal0.152.4
103103Etight thermal1.052.4
104104Etight thermal0.092.4
105105Etight thermal0.112.4
106106Ftight thermal0.132.4
107107Ftight thermal0.212.4
108108Ftight thermal0.182.4
109109Ftight thermal0.132.4
110110Ftight thermal0.162.4
111111Ftight thermal0.132.4
112112Ftight thermal0.122.4
113113Ftight thermal0.972.4
114114Ftight thermal1.052.4
115115Ftight thermal0.122.4
116116Ftight thermal1.042.4
117117Ftight thermal0.182.4
118118Ftight thermal0.182.4
119119Ftight thermal0.192.4
120120Ftight thermal0.182.4
121121Ftight thermal1.042.4
122122Ftight thermal0.142.4
123123Ftight thermal0.142.4
124124Gtight thermal0.182.4
125125Gtight thermal0.182.4
126126Gtight thermal0.142.4
127127Gtight thermal0.112.4
128128Gtight thermal0.082.4
129129Gtight thermal0.072.4
130130Gtight thermal0.982.4
131131Gtight thermal1.062.4
132132Gtight thermal0.092.4
133133Gtight thermal1.052.4
134134Gtight thermal0.152.4
135135Gtight thermal0.162.4
136136Gtight thermal0.162.4
137137Gtight thermal0.142.4
138138Gtight thermal1.052.4
139139Gtight thermal0.092.4
140140Gtight thermal0.092.4
141141Htight thermal0.282.4
142142Htight thermal0.22.4
143143Htight thermal0.152.4
144144Htight thermal0.182.4
145145Htight thermal0.172.4
146146Htight thermal12.4
147147Htight thermal1.072.4
148148Htight thermal0.182.4
149149Htight thermal1.062.4
150150Htight thermal0.112.4
151151Htight thermal0.12.4
152152Htight thermal0.132.4
153153Htight thermal0.112.4
154154Htight thermal1.062.4
155155Htight thermal0.162.4
156156Htight thermal0.182.4
157157Itight thermal0.152.4
158158Itight thermal0.222.4
159159Itight thermal0.182.4
160160Itight thermal0.192.4
161161Itight thermal0.992.4
162162Itight thermal1.062.4
163163Itight thermal0.172.4
164164Itight thermal1.062.4
165165Itight thermal0.252.4
166166Itight thermal0.252.4
167167Itight thermal0.262.4
168168Itight thermal0.242.4
169169Itight thermal1.062.4
170170Itight thermal0.192.4
171171Itight thermal0.22.4
172172Jtight thermal0.162.4
173173Jtight thermal0.122.4
174174Jtight thermal0.122.4
175175Jtight thermal0.972.4
176176Jtight thermal1.052.4
177177Jtight thermal0.112.4
178178Jtight thermal1.042.4
179179Jtight thermal0.182.4
180180Jtight thermal0.172.4
181181Jtight thermal0.192.4
182182Jtight thermal0.172.4
183183Jtight thermal1.042.4
184184Jtight thermal0.132.4
185185Jtight thermal0.162.4
186186Ktight thermal0.122.4
187187Ktight thermal0.12.4
188188Ktight thermal0.992.4
189189Ktight thermal1.062.4
190190Ktight thermal0.112.4
191191Ktight thermal1.062.4
192192Ktight thermal0.132.4
193193Ktight thermal0.152.4
194194Ktight thermal0.162.4
195195Ktight thermal0.152.4
196196Ktight thermal1.062.4
197197Ktight thermal0.112.4
198198Ktight thermal0.122.4
199199Ltight thermal0.072.4
200200Ltight thermal0.982.4
201201Ltight thermal1.062.4
202202Ltight thermal0.082.4
203203Ltight thermal1.052.4
204204Ltight thermal0.162.4
205205Ltight thermal0.162.4
206206Ltight thermal0.172.4
207207Ltight thermal0.152.4
208208Ltight thermal1.052.4
209209Ltight thermal0.112.4
210210Ltight thermal0.122.4
211211Mtight thermal0.982.4
212212Mtight thermal1.062.4
213213Mtight thermal0.072.4
214214Mtight thermal1.052.4
215215Mtight thermal0.142.4
216216Mtight thermal0.152.4
217217Mtight thermal0.162.4
218218Mtight thermal0.142.4
219219Mtight thermal1.062.4
220220Mtight thermal0.092.4
221221Mtight thermal0.112.4
222222Ntight thermal0.132.4
223223Ntight thermal0.982.4
224224Ntight thermal0.122.4
225225Ntight thermal0.992.4
226226Ntight thermal0.992.4
227227Ntight thermal0.982.4
228228Ntight thermal0.992.4
229229Ntight thermal0.112.4
230230Ntight thermal0.982.4
231231Ntight thermal0.992.4
232232Otight thermal1.052.4
233233Otight thermal0.082.4
234234Otight thermal1.062.4
235235Otight thermal1.072.4
236236Otight thermal1.062.4
237237Otight thermal1.072.4
238238Otight thermal0.112.4
239239Otight thermal1.062.4
240240Otight thermal1.062.4
241241Ptight thermal1.042.4
242242Ptight thermal0.162.4
243243Ptight thermal0.162.4
244244Ptight thermal0.172.4
245245Ptight thermal0.152.4
246246Ptight thermal1.052.4
247247Ptight thermal0.092.4
248248Ptight thermal0.112.4
249249Qtight thermal1.062.4
250250Qtight thermal1.062.4
251251Qtight thermal1.052.4
252252Qtight thermal1.062.4
253253Qtight thermal0.12.4
254254Qtight thermal1.052.4
255255Qtight thermal1.062.4
256256Rtight thermal0.092.4
257257Rtight thermal0.112.4
258258Rtight thermal0.082.4
259259Rtight thermal1.062.4
260260Rtight thermal0.152.4
261261Rtight thermal0.152.4
262262Stight thermal0.122.4
263263Stight thermal0.092.4
264264Stight thermal1.062.4
265265Stight thermal0.162.4
266266Stight thermal0.172.4
267267Ttight thermal0.112.4
268268Ttight thermal1.052.4
269269Ttight thermal0.162.4
270270Ttight thermal0.162.4
271271Utight thermal1.062.4
272272Utight thermal0.142.4
273273Utight thermal0.152.4
274274Utight thermal1.052.4
275275Vtight thermal1.062.4
276276Wtight thermal0.12.4
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork3.076 207865 -
obs--100 %

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