7VD8

1.96 A structure of human apoferritin obtained from Talos Arctica microscope


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI.

Fan, H.Wang, B.Zhang, Y.Zhu, Y.Song, B.Xu, H.Zhai, Y.Qiao, M.Sun, F.

(2021) Nat Commun 12: 7257-7257

  • DOI: https://doi.org/10.1038/s41467-021-27596-8
  • Primary Citation of Related Structures:  
    7VD8, 7VD9, 7VDA, 7VDC, 7VDE, 7VDF

  • PubMed Abstract: 

    Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, dissociation or denaturation of biomacromolecules during cryo-vitrification remains a limiting factor for many specimens. To solve this bottleneck, we developed a cryo-EM support film using 2D crystals of hydrophobin HFBI. The hydrophilic side of the HFBI film adsorbs protein particles via electrostatic interactions and sequesters them from the air-water interface, allowing the formation of sufficiently thin ice for high-quality data collection. The particle orientation distribution can be regulated by adjusting the buffer pH. Using this support, we determined the cryo-EM structures of catalase (2.29 Å) and influenza haemagglutinin trimer (2.56 Å), which exhibited strong preferred orientations using a conventional cryo-vitrification protocol. We further show that the HFBI film is suitable to obtain high-resolution structures of small proteins, including aldolase (150 kDa, 3.28 Å) and haemoglobin (64 kDa, 3.6 Å). Our work suggests that HFBI films may have broad future applications in increasing the success rate and efficiency of cryo-EM.


  • Organizational Affiliation

    National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
172Homo sapiensMutation(s): 0 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
GTEx:  ENSG00000167996 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth D]
AD [auth F]
AE [auth H]
AA [auth A],
AB [auth B],
AC [auth D],
AD [auth F],
AE [auth H],
AG [auth K],
AH [auth M],
AI [auth O],
AJ [auth Q],
AK [auth S],
AM [auth W],
BA [auth A],
BB [auth B],
BC [auth D],
BE [auth H],
BF [auth I],
BH [auth M],
BI [auth O],
BJ [auth Q],
BK [auth S],
BL [auth U],
BM [auth W],
CA [auth A],
CB [auth B],
CC [auth D],
CD [auth F],
CE [auth H],
CG [auth K],
CI [auth O],
CL [auth U],
CM [auth W],
DD [auth F],
DE [auth H],
DF [auth I],
DG [auth K],
DH [auth M],
DJ [auth Q],
DK [auth S],
DL [auth U],
DM [auth X],
EA [auth A],
EB [auth C],
EC [auth D],
ED [auth F],
EE [auth H],
EF [auth J],
EH [auth M],
EI [auth O],
EK [auth S],
EL [auth U],
EM [auth X],
FA [auth A],
FB [auth C],
FC [auth D],
FD [auth F],
FG [auth K],
FI [auth O],
FJ [auth Q],
FK [auth S],
FL [auth U],
GA [auth A],
GB [auth C],
GC [auth D],
GD [auth F],
GE [auth H],
GF [auth J],
GG [auth K],
GH [auth M],
GJ [auth Q],
GK [auth S],
GM [auth X],
HB [auth C],
HC [auth D],
HD [auth F],
HE [auth H],
HF [auth J],
HG [auth L],
HI [auth O],
HJ [auth Q],
HK [auth S],
HL [auth V],
HM [auth X],
IA [auth A],
IB [auth C],
ID [auth F],
IE [auth H],
IG [auth L],
IH [auth M],
II [auth O],
IJ [auth Q],
IK [auth T],
IL [auth V],
JA [auth A],
JC [auth E],
JD [auth F],
JF [auth J],
JG [auth L],
JH [auth M],
JJ [auth Q],
JL [auth V],
JM [auth X],
KA [auth A],
KB [auth C],
KC [auth E],
KD [auth F],
KE [auth H],
KF [auth J],
KG [auth L],
KI [auth O],
KJ [auth R],
KK [auth T],
KM [auth X],
LA [auth A],
LB [auth C],
LC [auth E],
LE [auth H],
LF [auth J],
LH [auth N],
LI [auth O],
LJ [auth R],
LK [auth T],
LL [auth V],
LM [auth X],
MB [auth C],
MC [auth E],
ME [auth H],
MF [auth J],
MG [auth L],
MH [auth N],
MI [auth P],
MJ [auth R],
MM [auth X],
NA [auth A],
ND [auth G],
NF [auth J],
NG [auth L],
NI [auth P],
NK [auth T],
NL [auth V],
NM [auth X],
OA [auth B],
OB [auth C],
OC [auth E],
OD [auth G],
OE [auth I],
OF [auth J],
OG [auth L],
OH [auth N],
OJ [auth R],
OL [auth V],
OM [auth X],
PA [auth B],
PB [auth C],
PC [auth E],
PD [auth G],
PE [auth I],
PF [auth J],
PH [auth N],
PI [auth P],
PK [auth T],
PL [auth V],
QA [auth B],
QB [auth C],
QC [auth E],
QD [auth G],
QE [auth I],
QF [auth J],
QG [auth L],
QH [auth N],
QI [auth P],
QJ [auth R],
QK [auth T],
QL [auth V],
RA [auth B],
RB [auth C],
RD [auth G],
RE [auth I],
RG [auth L],
RH [auth N],
RK [auth T],
RL [auth V],
SA [auth B],
SC [auth E],
SG [auth L],
SH [auth N],
SI [auth P],
SJ [auth R],
SK [auth T],
SL [auth W],
TB [auth C],
TC [auth E],
TD [auth G],
TE [auth I],
TF [auth K],
TH [auth N],
TI [auth P],
TJ [auth R],
TK [auth T],
TL [auth W],
UA [auth B],
UB [auth D],
UC [auth E],
UD [auth G],
UE [auth I],
UF [auth K],
UG [auth L],
UH [auth N],
UI [auth P],
UJ [auth R],
UK [auth T],
VA [auth B],
VB [auth D],
VE [auth I],
VF [auth K],
VH [auth N],
VI [auth P],
VJ [auth R],
VK [auth U],
VL [auth W],
WA [auth B],
WB [auth D],
WC [auth E],
WD [auth G],
WF [auth K],
WI [auth P],
WJ [auth R],
WK [auth U],
WL [auth W],
XB [auth D],
XD [auth G],
XE [auth I],
XF [auth K],
XG [auth M],
XH [auth O],
XJ [auth S],
Y [auth A],
YA [auth B],
YB [auth D],
YE [auth I],
YG [auth M],
YI [auth Q],
YJ [auth S],
YK [auth U],
YL [auth W],
Z [auth A],
ZA [auth B],
ZC [auth F],
ZD [auth G],
ZE [auth I],
ZF [auth K],
ZG [auth M],
ZH [auth O],
ZK [auth U],
ZL [auth W]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AF [auth I]
AL [auth U]
BD [auth F]
BG [auth K]
CF [auth I]
AF [auth I],
AL [auth U],
BD [auth F],
BG [auth K],
CF [auth I],
CH [auth M],
CJ [auth Q],
CK [auth S],
DA [auth A],
DB [auth B],
DC [auth D],
DI [auth O],
EG [auth K],
EJ [auth Q],
FE [auth H],
FF [auth J],
FH [auth M],
FM [auth X],
GI [auth O],
GL [auth V],
HA [auth A],
HH [auth M],
IC [auth D],
IF [auth J],
IM [auth X],
JB [auth C],
JE [auth H],
JI [auth O],
JK [auth T],
KH [auth N],
KL [auth V],
LD [auth F],
LG [auth L],
MA [auth A],
MD [auth G],
MK [auth T],
ML [auth V],
NB [auth C],
NC [auth E],
NE [auth H],
NH [auth N],
NJ [auth R],
OI [auth P],
OK [auth T],
PG [auth L],
PJ [auth R],
RC [auth E],
RF [auth J],
RI [auth P],
RJ [auth R],
SB [auth C],
SD [auth G],
SE [auth I],
SF [auth K],
TA [auth B],
TG [auth L],
UL [auth W],
VC [auth E],
VD [auth G],
VG [auth L],
WE [auth I],
WG [auth M],
WH [auth N],
XA [auth B],
XC [auth E],
XI [auth P],
XK [auth U],
XL [auth W],
YC [auth F],
YD [auth G],
YF [auth K],
YH [auth O],
ZB [auth D],
ZI [auth Q],
ZJ [auth S]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0504700
National Natural Science Foundation of China (NSFC)China31830020
Chinese Academy of SciencesChinaXDB37040102
National Natural Science Foundation of China (NSFC)China31925026
Ministry of Science and Technology (MoST, China)China2015DFG32140

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release