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- PDB-7r5o: 1.58 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2... -

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Basic information

Entry
Database: PDB / ID: 7r5o
Title1.58 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2 AT eBIC, DLS UNDER COMMISSIONING SESSION CM26464-2
ComponentsFerritin heavy chain, N-terminally processed
KeywordsMETAL BINDING PROTEIN / Protein standard
Function / homology
Function and homology information


iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.58 Å
AuthorsClare, D.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not fundedcm26464-2 United Kingdom
CitationJournal: Faraday Discuss / Year: 2022
Title: Application of super-resolution and correlative double sampling in cryo-electron microscopy.
Authors: Yuewen Sheng / Peter J Harrison / Vinod Vogirala / Zhengyi Yang / Claire Strain-Damerell / Thomas Frosio / Benjamin A Himes / C Alistair Siebert / Peijun Zhang / Daniel K Clare /
Abstract: Developments in cryo-EM have allowed atomic or near-atomic resolution structure determination to become routine in single particle analysis (SPA). However, near-atomic resolution structures ...Developments in cryo-EM have allowed atomic or near-atomic resolution structure determination to become routine in single particle analysis (SPA). However, near-atomic resolution structures determined using cryo-electron tomography and sub-tomogram averaging (cryo-ET STA) are much less routine. In this paper, we show that collecting cryo-ET STA data using the same conditions as SPA, with both correlated double sampling (CDS) and the super-resolution mode, allowed apoferritin to be reconstructed out to the physical Nyquist frequency of the images. Even with just two tilt series, STA yields an apoferritin map at 2.9 Å resolution. These results highlight the exciting potential of cryo-ET STA in the future of protein structure determination. While processing SPA data recorded in super-resolution mode may yield structures surpassing the physical Nyquist limit, processing cryo-ET STA data in the super-resolution mode gave no additional resolution benefit. We further show that collecting SPA data in the super-resolution mode, with CDS activated, reduces the estimated -factor, leading to a reduction in the number of particles required to reach a target resolution without compromising the data size on disk and the area imaged in SerialEM. However, collecting SPA data in CDS does reduce throughput, given that a similar resolution structure, with a slightly larger -factor, is achievable with optimised parameters for speed in EPU (without CDS).
History
DepositionFeb 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
I: Ferritin heavy chain, N-terminally processed
J: Ferritin heavy chain, N-terminally processed
K: Ferritin heavy chain, N-terminally processed
L: Ferritin heavy chain, N-terminally processed
M: Ferritin heavy chain, N-terminally processed
N: Ferritin heavy chain, N-terminally processed
O: Ferritin heavy chain, N-terminally processed
P: Ferritin heavy chain, N-terminally processed
Q: Ferritin heavy chain, N-terminally processed
R: Ferritin heavy chain, N-terminally processed
S: Ferritin heavy chain, N-terminally processed
T: Ferritin heavy chain, N-terminally processed
U: Ferritin heavy chain, N-terminally processed
V: Ferritin heavy chain, N-terminally processed
W: Ferritin heavy chain, N-terminally processed
X: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,79748
Polymers485,24624
Non-polymers55224
Water60,9633384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron 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
1010A4 - 176
2010B4 - 176
1020A4 - 176
2020C4 - 176
1030A4 - 176
2030D4 - 176
1040A4 - 176
2040E4 - 176
1050A4 - 176
2050F4 - 176
1060A4 - 176
2060G4 - 176
1070A4 - 176
2070H4 - 176
1080A4 - 176
2080I4 - 176
1090A4 - 176
2090J4 - 176
10100A4 - 176
20100K4 - 176
10110A4 - 176
20110L4 - 176
10120A4 - 176
20120M4 - 176
10130A4 - 176
20130N4 - 176
10140A4 - 176
20140O4 - 176
10150A4 - 176
20150P4 - 176
10160A4 - 176
20160Q4 - 176
10170A4 - 176
20170R4 - 176
10180A4 - 176
20180S4 - 176
10190A4 - 176
20190T4 - 176
10200A4 - 176
20200U4 - 176
10210A4 - 176
20210V4 - 176
10220A4 - 176
20220W4 - 176
10230A4 - 176
20230X4 - 176
10240B4 - 176
20240C4 - 176
10250B4 - 176
20250D4 - 176
10260B4 - 176
20260E4 - 176
10270B4 - 176
20270F4 - 176
10280B4 - 176
20280G4 - 176
10290B4 - 176
20290H4 - 176
10300B4 - 176
20300I4 - 176
10310B4 - 176
20310J4 - 176
10320B4 - 176
20320K4 - 176
10330B4 - 176
20330L4 - 176
10340B4 - 176
20340M4 - 176
10350B4 - 176
20350N4 - 176
10360B4 - 176
20360O4 - 176
10370B4 - 176
20370P4 - 176
10380B4 - 176
20380Q4 - 176
10390B4 - 176
20390R4 - 176
10400B4 - 176
20400S4 - 176
10410B4 - 176
20410T4 - 176
10420B4 - 176
20420U4 - 176
10430B4 - 176
20430V4 - 176
10440B4 - 176
20440W4 - 176
10450B4 - 176
20450X4 - 176
10460C4 - 176
20460D4 - 176
10470C4 - 176
20470E4 - 176
10480C4 - 176
20480F4 - 176
10490C4 - 176
20490G4 - 176
10500C4 - 176
20500H4 - 176
10510C4 - 176
20510I4 - 176
10520C4 - 176
20520J4 - 176
10530C4 - 176
20530K4 - 176
10540C4 - 176
20540L4 - 176
10550C4 - 176
20550M4 - 176
10560C4 - 176
20560N4 - 176
10570C4 - 176
20570O4 - 176
10580C4 - 176
20580P4 - 176
10590C4 - 176
20590Q4 - 176
10600C4 - 176
20600R4 - 176
10610C4 - 176
20610S4 - 176
10620C4 - 176
20620T4 - 176
10630C4 - 176
20630U4 - 176
10640C4 - 176
20640V4 - 176
10650C4 - 176
20650W4 - 176
10660C4 - 176
20660X4 - 176
10670D4 - 176
20670E4 - 176
10680D4 - 176
20680F4 - 176
10690D4 - 176
20690G4 - 176
10700D4 - 176
20700H4 - 176
10710D4 - 176
20710I4 - 176
10720D4 - 176
20720J4 - 176
10730D4 - 176
20730K4 - 176
10740D4 - 176
20740L4 - 176
10750D4 - 176
20750M4 - 176
10760D4 - 176
20760N4 - 176
10770D4 - 176
20770O4 - 176
10780D4 - 176
20780P4 - 176
10790D4 - 176
20790Q4 - 176
10800D4 - 176
20800R4 - 176
10810D4 - 176
20810S4 - 176
10820D4 - 176
20820T4 - 176
10830D4 - 176
20830U4 - 176
10840D4 - 176
20840V4 - 176
10850D4 - 176
20850W4 - 176
10860D4 - 176
20860X4 - 176
10870E4 - 176
20870F4 - 176
10880E4 - 176
20880G4 - 176
10890E4 - 176
20890H4 - 176
10900E4 - 176
20900I4 - 176
10910E4 - 176
20910J4 - 176
10920E4 - 176
20920K4 - 176
10930E4 - 176
20930L4 - 176
10940E4 - 176
20940M4 - 176
10950E4 - 176
20950N4 - 176
10960E4 - 176
20960O4 - 176
10970E4 - 176
20970P4 - 176
10980E4 - 176
20980Q4 - 176
10990E4 - 176
20990R4 - 176
101000E4 - 176
201000S4 - 176
101010E4 - 176
201010T4 - 176
101020E4 - 176
201020U4 - 176
101030E4 - 176
201030V4 - 176
101040E4 - 176
201040W4 - 176
101050E4 - 176
201050X4 - 176
101060F4 - 176
201060G4 - 176
101070F4 - 176
201070H4 - 176
101080F4 - 176
201080I4 - 176
101090F4 - 176
201090J4 - 176
101100F4 - 176
201100K4 - 176
101110F4 - 176
201110L4 - 176
101120F4 - 176
201120M4 - 176
101130F4 - 176
201130N4 - 176
101140F4 - 176
201140O4 - 176
101150F4 - 176
201150P4 - 176
101160F4 - 176
201160Q4 - 176
101170F4 - 176
201170R4 - 176
101180F4 - 176
201180S4 - 176
101190F4 - 176
201190T4 - 176
101200F4 - 176
201200U4 - 176
101210F4 - 176
201210V4 - 176
101220F4 - 176
201220W4 - 176
101230F4 - 176
201230X4 - 176
101240G4 - 176
201240H4 - 176
101250G4 - 176
201250I4 - 176
101260G4 - 176
201260J4 - 176
101270G4 - 176
201270K4 - 176
101280G4 - 176
201280L4 - 176
101290G4 - 176
201290M4 - 176
101300G4 - 176
201300N4 - 176
101310G4 - 176
201310O4 - 176
101320G4 - 176
201320P4 - 176
101330G4 - 176
201330Q4 - 176
101340G4 - 176
201340R4 - 176
101350G4 - 176
201350S4 - 176
101360G4 - 176
201360T4 - 176
101370G4 - 176
201370U4 - 176
101380G4 - 176
201380V4 - 176
101390G4 - 176
201390W4 - 176
101400G4 - 176
201400X4 - 176
101410H4 - 176
201410I4 - 176
101420H4 - 176
201420J4 - 176
101430H4 - 176
201430K4 - 176
101440H4 - 176
201440L4 - 176
101450H4 - 176
201450M4 - 176
101460H4 - 176
201460N4 - 176
101470H4 - 176
201470O4 - 176
101480H4 - 176
201480P4 - 176
101490H4 - 176
201490Q4 - 176
101500H4 - 176
201500R4 - 176
101510H4 - 176
201510S4 - 176
101520H4 - 176
201520T4 - 176
101530H4 - 176
201530U4 - 176
101540H4 - 176
201540V4 - 176
101550H4 - 176
201550W4 - 176
101560H4 - 176
201560X4 - 176
101570I4 - 176
201570J4 - 176
101580I4 - 176
201580K4 - 176
101590I4 - 176
201590L4 - 176
101600I4 - 176
201600M4 - 176
101610I4 - 176
201610N4 - 176
101620I4 - 176
201620O4 - 176
101630I4 - 176
201630P4 - 176
101640I4 - 176
201640Q4 - 176
101650I4 - 176
201650R4 - 176
101660I4 - 176
201660S4 - 176
101670I4 - 176
201670T4 - 176
101680I4 - 176
201680U4 - 176
101690I4 - 176
201690V4 - 176
101700I4 - 176
201700W4 - 176
101710I4 - 176
201710X4 - 176
101720J4 - 176
201720K4 - 176
101730J4 - 176
201730L4 - 176
101740J4 - 176
201740M4 - 176
101750J4 - 176
201750N4 - 176
101760J4 - 176
201760O4 - 176
101770J4 - 176
201770P4 - 176
101780J4 - 176
201780Q4 - 176
101790J4 - 176
201790R4 - 176
101800J4 - 176
201800S4 - 176
101810J4 - 176
201810T4 - 176
101820J4 - 176
201820U4 - 176
101830J4 - 176
201830V4 - 176
101840J4 - 176
201840W4 - 176
101850J4 - 176
201850X4 - 176
101860K4 - 176
201860L4 - 176
101870K4 - 176
201870M4 - 176
101880K4 - 176
201880N4 - 176
101890K4 - 176
201890O4 - 176
101900K4 - 176
201900P4 - 176
101910K4 - 176
201910Q4 - 176
101920K4 - 176
201920R4 - 176
101930K4 - 176
201930S4 - 176
101940K4 - 176
201940T4 - 176
101950K4 - 176
201950U4 - 176
101960K4 - 176
201960V4 - 176
101970K4 - 176
201970W4 - 176
101980K4 - 176
201980X4 - 176
101990L4 - 176
201990M4 - 176
102000L4 - 176
202000N4 - 176
102010L4 - 176
202010O4 - 176
102020L4 - 176
202020P4 - 176
102030L4 - 176
202030Q4 - 176
102040L4 - 176
202040R4 - 176
102050L4 - 176
202050S4 - 176
102060L4 - 176
202060T4 - 176
102070L4 - 176
202070U4 - 176
102080L4 - 176
202080V4 - 176
102090L4 - 176
202090W4 - 176
102100L4 - 176
202100X4 - 176
102110M4 - 176
202110N4 - 176
102120M4 - 176
202120O4 - 176
102130M4 - 176
202130P4 - 176
102140M4 - 176
202140Q4 - 176
102150M4 - 176
202150R4 - 176
102160M4 - 176
202160S4 - 176
102170M4 - 176
202170T4 - 176
102180M4 - 176
202180U4 - 176
102190M4 - 176
202190V4 - 176
102200M4 - 176
202200W4 - 176
102210M4 - 176
202210X4 - 176
102220N4 - 176
202220O4 - 176
102230N4 - 176
202230P4 - 176
102240N4 - 176
202240Q4 - 176
102250N4 - 176
202250R4 - 176
102260N4 - 176
202260S4 - 176
102270N4 - 176
202270T4 - 176
102280N4 - 176
202280U4 - 176
102290N4 - 176
202290V4 - 176
102300N4 - 176
202300W4 - 176
102310N4 - 176
202310X4 - 176
102320O4 - 176
202320P4 - 176
102330O4 - 176
202330Q4 - 176
102340O4 - 176
202340R4 - 176
102350O4 - 176
202350S4 - 176
102360O4 - 176
202360T4 - 176
102370O4 - 176
202370U4 - 176
102380O4 - 176
202380V4 - 176
102390O4 - 176
202390W4 - 176
102400O4 - 176
202400X4 - 176
102410P4 - 176
202410Q4 - 176
102420P4 - 176
202420R4 - 176
102430P4 - 176
202430S4 - 176
102440P4 - 176
202440T4 - 176
102450P4 - 176
202450U4 - 176
102460P4 - 176
202460V4 - 176
102470P4 - 176
202470W4 - 176
102480P4 - 176
202480X4 - 176
102490Q4 - 176
202490R4 - 176
102500Q4 - 176
202500S4 - 176
102510Q4 - 176
202510T4 - 176
102520Q4 - 176
202520U4 - 176
102530Q4 - 176
202530V4 - 176
102540Q4 - 176
202540W4 - 176
102550Q4 - 176
202550X4 - 176
102560R4 - 176
202560S4 - 176
102570R4 - 176
202570T4 - 176
102580R4 - 176
202580U4 - 176
102590R4 - 176
202590V4 - 176
102600R4 - 176
202600W4 - 176
102610R4 - 176
202610X4 - 176
102620S4 - 176
202620T4 - 176
102630S4 - 176
202630U4 - 176
102640S4 - 176
202640V4 - 176
102650S4 - 176
202650W4 - 176
102660S4 - 176
202660X4 - 176
102670T4 - 176
202670U4 - 176
102680T4 - 176
202680V4 - 176
102690T4 - 176
202690W4 - 176
102700T4 - 176
202700X4 - 176
102710U4 - 176
202710V4 - 176
102720U4 - 176
202720W4 - 176
102730U4 - 176
202730X4 - 176
102740V4 - 176
202740W4 - 176
102750V4 - 176
202750X4 - 176
102760W4 - 176
202760X4 - 176

NCS ensembles :
ID
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-
Components

#1: Protein ...
Ferritin heavy chain, N-terminally processed


Mass: 20218.570 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Details: Bacterial expression / Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: human Apoferritin / Type: COMPLEX / Details: Heavy chain / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: D3A
Buffer solutionpH: 7.5 / Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM TCEP
SpecimenConc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The apoferritin sample was applied to in-house graphene-coated Quantifoil r2/2 EM grid
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot time of 2.5 seconds

-
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 FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 34 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2295
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

-
Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13REFMACmodel refinement
CTF correctionDetails: Done in Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 1.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6Z6U
RefinementResolution: 1.6→132.51 Å / Cor.coef. Fo:Fc: 0.853 / SU B: 2.047 / SU ML: 0.061 / ESU R: 0.075
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.24461 --
obs0.24461 1189862 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 22.382 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Total: 38520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.020.01235976
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg2.4811.63348648
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.68954464
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.18623.832256
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.147156744
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.56715192
ELECTRON MICROSCOPYr_chiral_restr0.1930.24416
ELECTRON MICROSCOPYr_gen_planes_refined0.0140.0227936
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_it2.6961.55916992
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it4.3062.33121312
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it6.9792.42518984
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined13.20936.108185873
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A12674
12B12674
21A12674
22C12674
31A12674
32D12674
41A12674
42E12674
51A12670
52F12670
61A12672
62G12672
71A12672
72H12672
81A12644
82I12644
91A12644
92J12644
101A12644
102K12644
111A12644
112L12644
121A12644
122M12644
131A12644
132N12644
141A12644
142O12644
151A12644
152P12644
161A12672
162Q12672
171A12672
172R12672
181A12672
182S12672
191A12672
192T12672
201A12644
202U12644
211A12644
212V12644
221A12644
222W12644
231A12644
232X12644
241B12674
242C12674
251B12674
252D12674
261B12674
262E12674
271B12670
272F12670
281B12672
282G12672
291B12672
292H12672
301B12644
302I12644
311B12644
312J12644
321B12644
322K12644
331B12644
332L12644
341B12644
342M12644
351B12644
352N12644
361B12644
362O12644
371B12644
372P12644
381B12672
382Q12672
391B12672
392R12672
401B12672
402S12672
411B12672
412T12672
421B12644
422U12644
431B12644
432V12644
441B12644
442W12644
451B12644
452X12644
461C12674
462D12674
471C12674
472E12674
481C12670
482F12670
491C12672
492G12672
501C12672
502H12672
511C12646
512I12646
521C12644
522J12644
531C12646
532K12646
541C12644
542L12644
551C12644
552M12644
561C12644
562N12644
571C12644
572O12644
581C12644
582P12644
591C12672
592Q12672
601C12672
602R12672
611C12672
612S12672
621C12672
622T12672
631C12644
632U12644
641C12644
642V12644
651C12644
652W12644
661C12644
662X12644
671D12674
672E12674
681D12670
682F12670
691D12672
692G12672
701D12672
702H12672
711D12644
712I12644
721D12644
722J12644
731D12644
732K12644
741D12644
742L12644
751D12644
752M12644
761D12644
762N12644
771D12644
772O12644
781D12644
782P12644
791D12672
792Q12672
801D12672
802R12672
811D12672
812S12672
821D12672
822T12672
831D12644
832U12644
841D12644
842V12644
851D12644
852W12644
861D12644
862X12644
871E12670
872F12670
881E12672
882G12672
891E12672
892H12672
901E12644
902I12644
911E12644
912J12644
921E12644
922K12644
931E12644
932L12644
941E12644
942M12644
951E12644
952N12644
961E12644
962O12644
971E12644
972P12644
981E12672
982Q12672
991E12672
992R12672
1001E12672
1002S12672
1011E12672
1012T12672
1021E12644
1022U12644
1031E12644
1032V12644
1041E12644
1042W12644
1051E12644
1052X12644
1061F12670
1062G12670
1071F12670
1072H12670
1081F12642
1082I12642
1091F12642
1092J12642
1101F12642
1102K12642
1111F12642
1112L12642
1121F12642
1122M12642
1131F12642
1132N12642
1141F12642
1142O12642
1151F12642
1152P12642
1161F12670
1162Q12670
1171F12670
1172R12670
1181F12670
1182S12670
1191F12670
1192T12670
1201F12642
1202U12642
1211F12642
1212V12642
1221F12642
1222W12642
1231F12642
1232X12642
1241G12672
1242H12672
1251G12644
1252I12644
1261G12644
1262J12644
1271G12644
1272K12644
1281G12644
1282L12644
1291G12644
1292M12644
1301G12644
1302N12644
1311G12644
1312O12644
1321G12644
1322P12644
1331G12672
1332Q12672
1341G12672
1342R12672
1351G12672
1352S12672
1361G12672
1362T12672
1371G12644
1372U12644
1381G12644
1382V12644
1391G12644
1392W12644
1401G12644
1402X12644
1411H12644
1412I12644
1421H12644
1422J12644
1431H12644
1432K12644
1441H12644
1442L12644
1451H12644
1452M12644
1461H12644
1462N12644
1471H12644
1472O12644
1481H12644
1482P12644
1491H12672
1492Q12672
1501H12672
1502R12672
1511H12672
1512S12672
1521H12672
1522T12672
1531H12644
1532U12644
1541H12644
1542V12644
1551H12644
1552W12644
1561H12644
1562X12644
1571I12644
1572J12644
1581I12646
1582K12646
1591I12644
1592L12644
1601I12644
1602M12644
1611I12644
1612N12644
1621I12644
1622O12644
1631I12644
1632P12644
1641I12644
1642Q12644
1651I12644
1652R12644
1661I12644
1662S12644
1671I12644
1672T12644
1681I12644
1682U12644
1691I12644
1692V12644
1701I12644
1702W12644
1711I12644
1712X12644
1721J12644
1722K12644
1731J12644
1732L12644
1741J12644
1742M12644
1751J12644
1752N12644
1761J12644
1762O12644
1771J12644
1772P12644
1781J12644
1782Q12644
1791J12644
1792R12644
1801J12644
1802S12644
1811J12644
1812T12644
1821J12644
1822U12644
1831J12644
1832V12644
1841J12644
1842W12644
1851J12644
1852X12644
1861K12644
1862L12644
1871K12644
1872M12644
1881K12644
1882N12644
1891K12644
1892O12644
1901K12644
1902P12644
1911K12644
1912Q12644
1921K12644
1922R12644
1931K12644
1932S12644
1941K12644
1942T12644
1951K12644
1952U12644
1961K12644
1962V12644
1971K12644
1972W12644
1981K12644
1982X12644
1991L12644
1992M12644
2001L12644
2002N12644
2011L12644
2012O12644
2021L12644
2022P12644
2031L12644
2032Q12644
2041L12644
2042R12644
2051L12644
2052S12644
2061L12644
2062T12644
2071L12644
2072U12644
2081L12644
2082V12644
2091L12644
2092W12644
2101L12644
2102X12644
2111M12644
2112N12644
2121M12644
2122O12644
2131M12644
2132P12644
2141M12644
2142Q12644
2151M12644
2152R12644
2161M12644
2162S12644
2171M12644
2172T12644
2181M12644
2182U12644
2191M12644
2192V12644
2201M12644
2202W12644
2211M12644
2212X12644
2221N12644
2222O12644
2231N12644
2232P12644
2241N12644
2242Q12644
2251N12644
2252R12644
2261N12644
2262S12644
2271N12644
2272T12644
2281N12644
2282U12644
2291N12644
2292V12644
2301N12644
2302W12644
2311N12644
2312X12644
2321O12644
2322P12644
2331O12644
2332Q12644
2341O12644
2342R12644
2351O12644
2352S12644
2361O12644
2362T12644
2371O12644
2372U12644
2381O12644
2382V12644
2391O12644
2392W12644
2401O12644
2402X12644
2411P12644
2412Q12644
2421P12644
2422R12644
2431P12644
2432S12644
2441P12644
2442T12644
2451P12644
2452U12644
2461P12644
2462V12644
2471P12644
2472W12644
2481P12644
2482X12644
2491Q12672
2492R12672
2501Q12672
2502S12672
2511Q12672
2512T12672
2521Q12644
2522U12644
2531Q12644
2532V12644
2541Q12644
2542W12644
2551Q12644
2552X12644
2561R12672
2562S12672
2571R12672
2572T12672
2581R12644
2582U12644
2591R12644
2592V12644
2601R12644
2602W12644
2611R12644
2612X12644
2621S12672
2622T12672
2631S12644
2632U12644
2641S12644
2642V12644
2651S12644
2652W12644
2661S12644
2662X12644
2671T12644
2672U12644
2681T12644
2682V12644
2691T12644
2692W12644
2701T12644
2702X12644
2711U12644
2712V12644
2721U12644
2722W12644
2731U12644
2732X12644
2741V12644
2742W12644
2751V12644
2752X12644
2761W12642
2762X12642
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.687 87955 -
obs--100 %

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