A novel method for cryo-EM protein sample preparation based on Clear-Native-PAGE
Yang, Z., Kameo, S., Seki, S., Kurisu, G., Tanaka, R., Kawamoto, A., Takabayashi, A.To be published.
Experimental Data Snapshot
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chlorophyll a-b binding protein 6, chloroplastic | A [auth 1] | 241 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q01667 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I chlorophyll a/b-binding protein 2, chloroplastic | B [auth 2] | 257 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SYW8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic | C [auth 3] | 273 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SY97 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chlorophyll a-b binding protein 4, chloroplastic | D [auth 4] | 251 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P27521 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I P700 chlorophyll a apoprotein A1 | E [auth A] | 750 | Arabidopsis thaliana | Mutation(s): 0  EC: 1.97.1.12 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P56766 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I P700 chlorophyll a apoprotein A2 | F [auth B] | 734 | Arabidopsis thaliana | Mutation(s): 0  EC: 1.97.1.12 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P56767 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I iron-sulfur center | G [auth C] | 81 | Arabidopsis thaliana | Mutation(s): 0  EC: 1.97.1.12 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62090 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit II-2, chloroplastic | H [auth D] | 204 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SA56 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit IV A, chloroplastic | I [auth E] | 143 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9S831 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit III, chloroplastic | J [auth F] | 221 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SHE8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit V, chloroplastic | K [auth G] | 160 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9S7N7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 12 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit VI-2, chloroplastic | L [auth H] | 145 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SUI6 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 13 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit VIII | M [auth I] | 37 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P56768 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 14 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit IX | N [auth J] | 44 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P56769 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 15 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit psaK, chloroplastic | O [auth K] | 130 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SUI5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 16 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit XI, chloroplastic | P [auth L] | 219 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SUI4 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 17 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem I reaction center subunit N, chloroplastic | Q [auth N] | 171 | Arabidopsis thaliana | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P49107 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
| Ligands 12 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DGD (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | CF [auth B] | DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N | |||
| CHL (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | AB [auth 2] EB [auth 3] FC [auth 4] LC [auth 4] QB [auth 3] | CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M | |||
| CL0 (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | PD [auth A] | CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M | |||
| CLA (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | AD [auth A] AG [auth B] BD [auth A] BE [auth A] BG [auth B] | CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M | |||
| LMG (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | AH [auth J] KG [auth F] NH [auth N] OG [auth F] VG [auth G] | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N | |||
| LHG (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | HA [auth 1], KA [auth 1], MA [auth 2], UD [auth A] | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N | |||
| XAT (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | FA [auth 1], IA [auth 1], QA [auth 2] | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O4 SZCBXWMUOPQSOX-WVJDLNGLSA-N | |||
| A1LXP (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | GA [auth 1] GB [auth 3] JA [auth 1] LB [auth 3] TA [auth 2] | Lutein C40 H56 O2 KBPHJBAIARWVSC-RGZFRNHPSA-N | |||
| BCR (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | AC [auth 4] AE [auth A] AF [auth B] BF [auth B] CH [auth J] | BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N | |||
| PQN (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | WE [auth B], YD [auth A] | PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N | |||
| SF4 (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | IG [auth C], JG [auth C], OC [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N | |||
| UNL( Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | AA [auth 1] BA [auth 1] BB [auth 2] BC [auth 4] BH [auth J] | Unknown ligand LJBDFODJNLIPKO-UHFFFAOYSA-N | |||
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | RELION | 4.0.2 |
| MODEL REFINEMENT | Servalcat | 0.4.115 |
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | 23H04958 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 23H04960 |