[English] 日本語
Yorodumi
- PDB-2wsf: Improved Model of Plant Photosystem I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wsf
TitleImproved Model of Plant Photosystem I
Components
  • (PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN ...) x 2
  • (PHOTOSYSTEM I REACTION CENTER SUBUNIT ...) x 9
  • (PHOTOSYSTEM I-N ...) x 2
  • AT3G54890
  • CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC
  • LHCA3
  • PHOTOSYSTEM I IRON-SULFUR CENTER
  • TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I
KeywordsPHOTOSYNTHESIS / ELECTRON TRANSFER / MEMBRANE PROTEINS / LARGE COMPLEXES
Function / homology
Function and homology information


response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I ...response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / molecular adaptor activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Chlorophyll A-B binding protein fold / Chlorophyll A-B binding protein / Chlorophyll a-b binding protein like / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Photosystem I, reaction centre, subunit PsaF ...Chlorophyll A-B binding protein fold / Chlorophyll A-B binding protein / Chlorophyll a-b binding protein like / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / GTP Cyclohydrolase I; Chain A, domain 1 / Single helix bin / 4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / SH3 type barrels. - #50 / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Alpha-Beta Plaits - #20 / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Few Secondary Structures / Irregular / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / BETA-CAROTENE / CHLOROPHYLL A / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 ...sucrose / BETA-CAROTENE / CHLOROPHYLL A / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Chlorophyll a-b binding protein 6, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I-N subunit / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
PISUM SATIVUM (garden pea)
GLYCINE MAX (soybean)
SPINACIA OLERACEA (spinach)
HORDEUM VULGARE (barley)
PHASEOLUS VULGARIS (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.48 Å
AuthorsAmunts, A. / Toporik, H. / Borovikov, A. / Nelson, N.
CitationJournal: J. Biol. Chem. / Year: 2010
Title: Structure determination and improved model of plant photosystem I.
Authors: Amunts, A. / Toporik, H. / Borovikova, A. / Nelson, N.
History
DepositionSep 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Mar 2, 2016Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Other
Revision 2.0Nov 21, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_asym.entity_id
Revision 3.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _database_PDB_caveat.text / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_asym.entity_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 4.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: AT3G54890
2: TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I
3: LHCA3
4: CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC
A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTIC
E: PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTIC
F: PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTIC
G: PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTIC
H: PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTIC
I: PHOTOSYSTEM I REACTION CENTER SUBUNIT VIII
J: PHOTOSYSTEM I REACTION CENTER SUBUNIT IX
K: PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTIC
L: PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTIC
N: PHOTOSYSTEM I-N SUBUNIT
R: PHOTOSYSTEM I-N SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)649,036275
Polymers454,17018
Non-polymers194,866257
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.200, 190.200, 130.300
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 5 types, 5 molecules 1234C

#1: Protein AT3G54890 / LHCA1


Mass: 26021.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / References: UniProt: Q9C5R7, UniProt: Q01667*PLUS
#2: Protein TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I / LHCA2


Mass: 28926.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: Q41038
#3: Protein LHCA3


Mass: 29852.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GLYCINE MAX (soybean) / References: UniProt: C6TEX2*PLUS
#4: Protein CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC / LHCI TYPE III CAB-P4 LHCA4


Mass: 27181.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: Q9SQL2
#7: Protein PHOTOSYSTEM I IRON-SULFUR CENTER / / PSAC / PHOTOSYSTEM I SUBUNIT VII / 9 KDA POLYPEPTIDE / PSI-C


Mass: 8991.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P10793

-
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN ... , 2 types, 2 molecules AB

#5: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1 / / PSAA / PSI-A


Mass: 84284.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P05310
#6: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2 / / PSAB / PSI-B


Mass: 82490.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P05311

-
PHOTOSYSTEM I REACTION CENTER SUBUNIT ... , 9 types, 9 molecules DEFGHIJKL

#8: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTIC / / PSAD / PHOTOSYSTEM I 20 KDA SUBUNIT / PSI-D


Mass: 23170.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12353
#9: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTIC / / PSAE / PSI-E A


Mass: 14984.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / References: UniProt: Q9S831
#10: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTIC / / PSAF / LIGHT-HARVESTING COMPLEX I 17 KDA PROTEIN / PSI-F


Mass: 25445.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12355
#11: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTIC / / PSAG / PSI-G / PHOTOSYSTEM I 9 KDA PROTEIN


Mass: 18232.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12357
#12: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTIC / / PSAH / PSI-H / LIGHT-HARVESTING COMPLEX I 11 KDA PROTEIN


Mass: 15341.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P22179
#13: Protein/peptide PHOTOSYSTEM I REACTION CENTER SUBUNIT VIII / / PSAI / PSI-I


Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P17227
#14: Protein/peptide PHOTOSYSTEM I REACTION CENTER SUBUNIT IX / / PSAJ / PSI-J


Mass: 5079.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P17230
#15: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTIC / / PSAK / PHOTOSYSTEM I SUBUNIT X / PSI-K / LIGHT-HARVESTING COMPLEX I 7 KDA PROTEIN


Mass: 13742.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HORDEUM VULGARE (barley) / References: UniProt: P36886
#16: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTIC / / PSAL / PSI-L / PSI SUBUNIT V


Mass: 22957.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: Q41385

-
PHOTOSYSTEM I-N ... , 2 types, 2 molecules NR

#17: Protein PHOTOSYSTEM I-N SUBUNIT / / PSAN / PSI-N


Mass: 18460.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PHASEOLUS VULGARIS (French bean) / References: UniProt: Q84U30
#18: Protein PHOTOSYSTEM I-N SUBUNIT /


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea)

-
Sugars , 2 types, 61 molecules

#19: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#21: Sugar...
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 6 types, 196 molecules

#20: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 173 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56
#23: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#24: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#25: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#26: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically

-
Details

Sequence detailsSQUENCE MAPPING FOR CHAIN 3 MATCHES GB ACU20374

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 6
Details: 22.5 MM MES, BIS-TRIS PH 6, 10MM SUCCINIC ACID, 6% PEG6000, 0.015% DTM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 27, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 72787 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.1
Reflection shellResolution: 3.5→3.6 Å / % possible all: 78.5

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.48→50 Å / Cor.coef. Fo:Fc: 0.73 / Cor.coef. Fo:Fc free: 0.715 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.42517 1460 2 %RANDOM
Rwork0.39124 ---
obs0.39192 71237 96.4 %-
Displacement parametersBiso mean: 24.693 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å20 Å2-1.13 Å2
2---4.2 Å20 Å2
3---8.14 Å2
Refinement stepCycle: LAST / Resolution: 3.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24785 0 11248 0 36033
LS refinement shellResolution: 3.475→3.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 61 -
Rwork0.409 3726 -
obs--67.88 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • 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

-
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

Read more