PDB entry 4y28

View 4y28 on RCSB PDB site
Description: The structure of plant photosystem I super-complex at 2.8 angstrom resolution.
Class: photosynthesis
Keywords: photosynthesis, light harvesting, antenna, reaction center
Deposited on 2015-02-09, released 2015-08-19
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-04-24, with a file datestamp of 2019-04-19.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: Light-harvesting complex I chlorophyll A/B-binding protein
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28
    Domains in SCOPe 2.08: d4y281_
  • Chain '2':
    Compound: Type II chlorophyll a/b binding protein from photosystem I
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q41038
      • engineered mutation (132)
    Domains in SCOPe 2.08: d4y282_
  • Chain '3':
    Compound: Chlorophyll a-b binding protein 3, chloroplastic
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4y283_
  • Chain '4':
    Compound: chlorophyll a-b binding protein p4, chloroplastic
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9SQL2
      • engineered mutation (127)
    Domains in SCOPe 2.08: d4y284_
  • Chain 'A':
    Compound: photosystem I p700 chlorophyll a apoprotein a1
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P05310 (Start-757)
      • engineered mutation (20-21)
      • engineered mutation (116)
      • engineered mutation (219)
    Domains in SCOPe 2.08: d4y28a_
  • Chain 'B':
    Compound: photosystem I p700 chlorophyll a apoprotein a2
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P05311 (Start-732)
      • engineered mutation (4)
      • engineered mutation (114)
      • engineered mutation (272)
      • engineered mutation (470)
      • engineered mutation (475-476)
      • engineered mutation (634)
    Domains in SCOPe 2.08: d4y28b_
  • Chain 'C':
    Compound: photosystem I iron-sulfur center
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4y28c_
  • Chain 'D':
    Compound: photosystem I reaction center subunit II, chloroplastic
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28 (Start-140)
    Domains in SCOPe 2.08: d4y28d_
  • Chain 'E':
    Compound: photosystem I reaction center subunit IV a, chloroplastic
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28 (0-65)
    Domains in SCOPe 2.08: d4y28e1, d4y28e2
  • Chain 'F':
    Compound: Photosystem I reaction center subunit III
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28
    Domains in SCOPe 2.08: d4y28f_
  • Chain 'G':
    Compound: photosystem I reaction center
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28
  • Chain 'H':
    Compound: Photosystem I reaction center subunit VI
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28 (Start-83)
  • Chain 'I':
    Compound: Photosystem I reaction center subunit VIII
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: Photosystem I reaction center subunit IX
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4y28j_
  • Chain 'K':
    Compound: Photosystem I reaction center subunit X psaK
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28 (Start-78)
  • Chain 'L':
    Compound: Putative uncharacterized protein
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y28 (Start-166)
    Domains in SCOPe 2.08: d4y28l_
  • Heterogens: CL0, CLA, SF4, PQN, LHG, BCR, LMG, CA, DGD, LMU, LUT, CHL, ZEX

PDB Chain Sequences:

  • Chain '1':
    Sequence, based on SEQRES records: (download) 
    >4y281 (1:)
ftmtsedwmpgqprpsyldgsapgdfgfdplrlgevpenlerfkeselihcrwamlavpg
ilvpealglgnwvkaqewaalpggqatylgnpvpwgtlptilvieflsiafvehqrsmek
dpekkkypggafdplgyskdpkkfheykikevkngrlallafvgicvqqsaypgtgplen
lathladpwhnniginvlippq

    Sequence, based on observed residues (ATOM records): (download) 
    >4y281 (1:)
dwmpgqprpsyldgsapgdfgfdplrlgevpenlerfkeselihcrwamlavpgilvpea
lglgnwvkaqewaalpggqatylgnpvpwgtlptilvieflsiafvehqrsmekdpekkk
ypggafdplgyskdpkkfheykikevkngrlallafvgicvqqsaypgtgplenlathla
dpwhnniginvlip

  • Chain '2':
    Sequence, based on SEQRES records: (download) 
    >4y282 (2:)
masacassaiaavaistpssqkngspsgtskaflgrklkvnsstaspsrvrststvctva
epdrplwfpgstpppwldgslpgdfgfdplglgsdpeslrwnvqaelvhsrwamlgaagi
fipefltklgilltpswytageqeyftdtttlfivelvfigwaegrrwadilnpgcvntd
pifpnnkltgtdvgypgglwfdplgwgsaspqklkelrtkeikngrlamlavmgawfqhi
ytgtgpidnlfahladpghatifaaftpk

    Sequence, based on observed residues (ATOM records): (download) 
    >4y282 (2:)
vaepdrplwfpgstpppwldgslpgdfgfdplglgsdpeslrwnvqaelvhsrwamlgaa
gifipefltklgilltpswytageqeyftdtttlfivelvfigwaegrrwadilnpgcvn
tdpifpnnkltgtdvgypgglwfdplgwgsaspqklkelrtkeikngrlamlavmgawfq
hiytgtgpidnlfahladpghatifaa

  • Chain '3':
    Sequence, based on SEQRES records: (download) 
    >4y283 (3:)
matqalvssssltfaaeavrqsfrarslpssvgcsrkglvraaatppvkqggvdrplwfa
skqslsyldgslpgdygfdplglsdpegtggfieprwlaygevingrfamlgavgaiape
ylgkvglipqetalawfqtgvippagtynywadnytlfvlemalmgfaehrrfqdwakpg
smgkqyflglekgfggsgnpaypggpffnplgfgkdekslkelklkevkngrlamlailg
yfiqglvtgvgpyqnlldhvadpvnnnvltslkfh

    Sequence, based on observed residues (ATOM records): (download) 
    >4y283 (3:)
wfaskqslsyldgslpgdygfdplglsdpegtggfieprwlaygevingrfamlgavgai
apeylgkvglipqetalawfqtgvippagtynywadnytlfvlemalmgfaehrrfqdwa
kpgsmgkqyflglekgfggsgnpaypggpffnplgfgkdekslkelklkevkngrlamla
ilgyfiqglvtgvgpyqnlldhvadpvnnnvltsl

  • Chain '4':
    Sequence, based on SEQRES records: (download) 
    >4y284 (4:)
matvttqasaaifgpcglksrflggssgklnrgvafrpvgcspsasfkveakkgewlpgl
aspgyltgslpgdngfdplglaedpenlrwfvqaelvngrwamlgvagmllpevftsigi
invpkwydagkeeyfassstlfviefilshyveirrwqdiknpgsvnqdpifkqyslpag
evgypggifnplnfaptleakekeiangrlamlaflgfiiqhnvtgkgpfdnllqhisdp
whntivqtlggn

    Sequence, based on observed residues (ATOM records): (download) 
    >4y284 (4:)
kkgewlpglaspgyltgslpgdngfdplglaedpenlrwfvqaelvngrwamlgvagmll
pevftsigiinvpkwydagkeeyfassstlfviefilshyveirrwqdiknpgsvnqdpi
fkqyslpagevgypggifnplnfaptleakekeiangrlamlaflgfiiqhnvtgkgpfd
nllqhisdpwhntivqtl

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4y28A (A:)
miirspepkvqiladpevkiildrdpiktsfeqwakpghfsrtiakgpdtttwiwnlhad
ahdfdshtsdleeisrkvfsahfgqlsiiflwlsgmyfhgarfsnyeawlndpthirpsa
qvvwpivgqeilngdvgggfrgiqitsgffqiwrasgitselqlyctaigalvfaglmlf
agwfhyhkaapklawfqdvesmlnhhlagllglgslswaghqvhvslpinqflnagvdpk
eiplphefilnrdllaqlypsfaegatpfftlnwskyadfltfrggldpltgglwltdia
hhhlaiailfliaghmyrtnwgighgikdileahkgpftgqghkglyeilttswhaqlsi
nlamlgsltivvaqhmysmppypylatdyatqlslfthhmwiggflivgaaahaaifmvr
dydpttryndlldrvlrhrdaiishlnwvciflgfhsfglyihndtmsalgrpqdmfsdt
aiqlqpvfaqwiqnthalapgttapgatastsltwgggdlvavgnkvallpiplgtadfl
vhhihaftihvtvlillkgvlfarssrlipdkanlgfrfpcdgpgrggtcqvsawdhvfl
glfwmynsisvvifhfswkmqsdvwgtindqgvvthittgnfaqssitingwlrdflwaq
asqviqsygsslsayglfflgahfvwafslmflfsgrgywqeliesivwahnklkvapat
qpralsivqgravgvthyllggiattwafflariiavg

    Sequence, based on observed residues (ATOM records): (download) 
    >4y28A (A:)
evkiildrdpiktsfeqwakpghfsrtiakgpdtttwiwnlhadahdfdshtsdleeisr
kvfsahfgqlsiiflwlsgmyfhgarfsnyeawlndpthirpsaqvvwpivgqeilngdv
gggfrgiqitsgffqiwrasgitselqlyctaigalvfaglmlfagwfhyhkaapklawf
qdvesmlnhhlagllglgslswaghqvhvslpinqflnagvdpkeiplphefilnrdlla
qlypsfaegatpfftlnwskyadfltfrggldpltgglwltdiahhhlaiailfliaghm
yrtnwgighgikdileahkgpftgqghkglyeilttswhaqlsinlamlgsltivvaqhm
ysmppypylatdyatqlslfthhmwiggflivgaaahaaifmvrdydpttryndlldrvl
rhrdaiishlnwvciflgfhsfglyihndtmsalgrpqdmfsdtaiqlqpvfaqwiqnth
alapgttapgatastsltwgggdlvavgnkvallpiplgtadflvhhihaftihvtvlil
lkgvlfarssrlipdkanlgfrfpcdgpgrggtcqvsawdhvflglfwmynsisvvifhf
swkmqsdvwgtindqgvvthittgnfaqssitingwlrdflwaqasqviqsygsslsayg
lfflgahfvwafslmflfsgrgywqeliesivwahnklkvapatqpralsivqgravgvt
hyllggiattwafflariiavg

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4y28B (B:)
malrlprfsqgiaqdpttrriwfgiatahdfeshdditegrlyqnifashfgqlaiiflw
tsgnlfhvawqgnfeawvqdpfhvrpiahaiwdphfgqpaveaftrggalgpvniaysgv
yqwwytiglrtnedlytgaifllflsfisllagwlhlqpkwkpsvswfknaesrlnhhls
glfgvsslawaghlvhvaipgsrgeyvrwnnfldvlpypqglgplltgqwnlyaqnpsss
nhlfgttqgagtailtilggfhpqtqslwltdmahhhlaiaflfligglmyrtnfgighs
ikyileahippggrlgrghkglydtinnsihfqlglalaslgvitslvaqhmyslpayaf
iaqdfttqaalythhqyiagfimtgafahgpiffirdynpeqnadnvlarmlehkeaiis
hlswaslflgfhtlglyvhndvmlafgtpekqiliepifaqwiqsahgktsygfdvllss
tngpalnagrniwlpgwlnainensnslfltigpgdflvhhaialglhtttlilvkgald
argsklmpdkkdfgysfpcdgpgrggtcdisawddfylavfwmlntigwvtfywhwkhit
lwrgnvsqfnesstylmgwlrdylwlnssqlingytplvcnslsvwawmflfghlvwatg
fmfliswrgywqelietlawahertplanlirwrdkpvalsivqarlvglvhfsvgyift
yaafliastsgkf

    Sequence, based on observed residues (ATOM records): (download) 
    >4y28B (B:)
alrlprfsqgiaqdpttrriwfgiatahdfeshdditegrlyqnifashfgqlaiiflwt
sgnlfhvawqgnfeawvqdpfhvrpiahaiwdphfgqpaveaftrggalgpvniaysgvy
qwwytiglrtnedlytgaifllflsfisllagwlhlqpkwkpsvswfknaesrlnhhlsg
lfgvsslawaghlvhvaipgsrgeyvrwnnfldvlpypqglgplltgqwnlyaqnpsssn
hlfgttqgagtailtilggfhpqtqslwltdmahhhlaiaflfligglmyrtnfgighsi
kyileahippggrlgrghkglydtinnsihfqlglalaslgvitslvaqhmyslpayafi
aqdfttqaalythhqyiagfimtgafahgpiffirdynpeqnadnvlarmlehkeaiish
lswaslflgfhtlglyvhndvmlafgtpekqiliepifaqwiqsahgktsygfdvllsst
ngpalnagrniwlpgwlnainensnslfltigpgdflvhhaialglhtttlilvkgalda
rgsklmpdkkdfgysfpcdgpgrggtcdisawddfylavfwmlntigwvtfywhwkhitl
wrgnvsqfnesstylmgwlrdylwlnssqlingytplvcnslsvwawmflfghlvwatgf
mfliswrgywqelietlawahertplanlirwrdkpvalsivqarlvglvhfsvgyifty
aafliastsgkf

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4y28C (C:)
mshsvkiydtcigctqcvracptdvlemipwggckakqiasaprtedcvgckrcesacpt
dflsvrvylwhettrsmglay

    Sequence, based on observed residues (ATOM records): (download) 
    >4y28C (C:)
shsvkiydtcigctqcvracptdvlemipwggckakqiasaprtedcvgckrcesacptd
flsvrvylwhettrsmglay

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4y28D (D:)
keapvgtppeldpntpspifggstggllrkaqveefyvitwespkeqifemptggaaimr
egpnllklarkeqclalgtrlrskykikyqfyrvfpsgevqylhpkdgvypekvnpgrqg
vgvnfrsigknvspievkftgkqpydl

    Sequence, based on observed residues (ATOM records): (download) 
    >4y28D (D:)
tppeldpntpspifggstggllrkaqveefyvitwespkeqifemptggaaimregpnll
klarkeqclalgtrlrskykikyqfyrvfpsgevqylhpkdgvypekvnpgrqgvgvnfr
sigknvspievkftgkqpydl

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4y28E (E:)
ppigpkrgakvkilrqesywykgtgsvvtvdqdpntrypvvvrfnkvnyanvstnnyald
eveevk

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4y28F (F:)
disgltpckeskqfakrekqsikklesslkiyaadsapalainatiektkrrfdnyakqg
llcgadglphlivsgdqrhwgefitpgilflyiagwigwvgrsyliairdekkptqkeii
idvplasrlvfrgfswpiaayrellngelvakdv

    Sequence, based on observed residues (ATOM records): (download) 
    >4y28F (F:)
sgltpckeskqfakrekqsikklesslkiyaadsapalainatiektkrrfdnyakqgll
cgadglphlivsgdqrhwgefitpgilflyiagwigwvgrsyliairdekkptqkeiiid
vplasrlvfrgfswpiaayrellngelvak

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >4y28J (J:)
mrdlktylsvapvastlwfaalagllieinrlfpdaltfpff

    Sequence, based on observed residues (ATOM records): (download) 
    >4y28J (J:)
rdlktylsvapvastlwfaalagllieinrlfpdaltfpff

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >4y28L (L:)
avqsekptyqvvqpingdpfigsletpvtssplvawylsnlpgyrtavnpllrgievgla
hgfflvgpfvkagplrnteiagqagslaaaglvvilsicltiygissfnegdpstapslt
ltgrkkqpdqlqtadgwakftggfffggisgviwaffllyvldlpyy

    Sequence, based on observed residues (ATOM records): (download) 
    >4y28L (L:)
tyqvvqpingdpfigsletpvtssplvawylsnlpgyrtavnpllrgievglahgfflvg
pfvkagplrnteiagqagslaaaglvvilsicltiygissfnegdpstapsltltgrkkq
pdqlqtadgwakftggfffggisgviwaffllyvldlpyy