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9se6

Structure of Photosystem I from Chlamydomonas reinhardtii at 1.83 A resolution

Method: ELECTRON MICROSCOPY D_max: 174.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9se6
deposition_date	2025-08-15
title	Structure of Photosystem I from Chlamydomonas reinhardtii at 1.83 A resolution
keywords	Photosystem I, Chlamydomonas reinhardtii, CryoEM, PHOTOSYNTHESIS; PHOTOSYNTHESIS
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	60.25 Å
rg_electron	59.80 Å
i0	3405490000.00
molecular_weight	665000.0 kDa
excluded_volume	895450 Å³
envelope_volume	1076400 Å³
shell_volume	143130 Å³
envelope_diameter	188.1 Å
shell_rg	65.37 Å
envelope_rg	59.39 Å
shape_rg	59.82 Å
total_rg	59.85 Å
total_atoms	47459
n_residues	3993
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	174.9 Å
rg_real	60.04 Å
rg_real_error	0.93 Å
i0_real	3.4050e+09
i0_real_error	5.9800e+07
rg_reciprocal	60.40 Å
i0_reciprocal	3407000000.0000
total_estimate	0.8450
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	67.3 Å
skewness	0.179
kurtosis	-0.630
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	611000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.994; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.002

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4. Crystallography & Experiment

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5. Entities & Polymer Info (32)

Entity 1 polymer

description	Light-harvesting chlorophyll-a/b protein of photosystem I, type III
formula_weight	23888.2 kDa
mutation	No
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	3
atom_count	48478

QLYVGASQSSLAYLDGSLPGDFGFDPLGLLDPVNSGGFIEPKWLQYSEVIHARWAMLGAAGCIAPEVLGAAGLIPDATNIKWFESGVIPPAGSYNGYWADPYTIFFVEIVAMQFAELRRLQDFRYPGSMGQQYFLGLEAIFKGSGDAAYPGGPFFNLFNLGKTEAAMKELKLKEIKNGRLAMLAMLGYGAQAVMTGKGPFQNLVEHLADPVNNNILTNFAG

Entity 2 polymer

description	Chlorophyll a-b binding protein, chloroplastic
formula_weight	23304.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4

KRDAALPSWMPGADLPGYLNGTLPGDFGFDPLYLGQDPVKLKWYAQAELMNARFAMLAVAGILVPELLSNIGFSWPGAGVAWYDAGKFEYFAPASSLFGVQMLLFAWVEIRRYQDFVKPGSANQDPIFTNNKLPDGNEPGYPGGIFDPFGWSKGDIKSLKLKEIKNGRLAMLAFAGFIGQAYTTGTTPLKNLSTHLADPWSTTVWQNDLARL

Entity 3 polymer

description	Chlorophyll a-b binding protein, chloroplastic
formula_weight	25122.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	5

DRKLWAPGVVAPEYLKGDLAGDYGWDPLGLGADPTALKWYRQSELQHARWAMLGVAGVLVQEIVKPDVYFYEAGLPQNLPEPFTNINMGGLLAWEFILMHWVEVRRWQDYKNFGSVNEDPIFKGNKVPNPEMGYPGGIFDPFGFSKGNLKELQTKEIKNGRLAMIAYMAFILQAQATGKGPLAALSAHLSNPFGNNILKNIGTCTVPHSVDVQGLTIPLTCLWPGSQ

Entity 4 polymer

description	Chlorophyll a-b binding protein, chloroplastic
formula_weight	25025.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	6

SRPLWLPGSTPPAHLKGDLPGDFGFDPLGLGANAESLKWFKESELVHSRWAMAAVAGILVQEIVRPDVFWYNAGKEVESPLGPLGLLAVEFFLMHWVEVRRWQDLRKPGSVDQDPIFSQYKLPPHEVGYPGGVFAPFIPGDLAELKVKEIKNGRLAMLAFVGFVMAAQVTGKGPIAALQEHLADPWGTTIFSKAAVVPGQAVAPPCKIPASVSYKGIEIPTPCFLQGLWP

Entity 5 polymer

description	Chlorophyll a-b binding protein, chloroplastic
formula_weight	23304.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	7

VRPVWFPGNPPPAHLDGSLAGDYGFDPLFLGQEPQTLKWYVQAELVHGRFAMLGAAGIILTSIGAKVGLGFPEWYDAGKVVVEKNNIDFPTLMVIQFYLMGWAETKRWYDFKNPGSQADGSFLGFTEEFKGLENGYPGGRFFDPMGLSRGDAAKYQEYKQKEVKNGRLAMIACLGFAAQYAATGKGPLDNLADHLADPNHVNFATNGVSIPIA

Entity 6 polymer

description	Chlorophyll a-b binding protein, chloroplastic
formula_weight	23293.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	8

RQSWLPGSQIPAHLDTPAAQALAGNFGFDPLGLGKDPVALRWYQQAELIHCRTAMAGVAGILIPGLLTKAGALNVPEWYDAGKVAIENSFAPWGSLLAVQLFLCGFVEAKRWQDIRKPGSQGEPGSFLGFEASLKGTSELGYPGGPFDPLGLSKEADKWADWKLKEVKNGRLAMLAFLGFVAQKYATGAGPVDNLAAHLKDPWHVNYATNGVSLPFL

Entity 7 polymer

description	Photosystem I P700 chlorophyll a apoprotein A1
formula_weight	82193.0 kDa
ec_number	1.97.1.12
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

AKKVKIAVDRNPVETSFEKWAKPGHFSRTLSKGPNTTTWIWNLHADAHDFDSHTSDLEEISRKVFSAHFGQLGIIFIWLSGMYFHGARFSNYEAWLSDPTHIKPSAQVVWPIVGQEILNGDVGGGFQGIQITSGFFQLWRASGITSELQLYTTAIGGLVMAAAMFFAGWFHYHKAAPKLEWFQNVESMLNHHLGGLLGLGSLAWAGHQIHVSLPVNKLLDAGVDPKEIPLPHDLLLNRAIMADLYPSFAKGIAPFFTLNWSEYSDFLTFKGGLNPVTGGLWLSDTAHHHVAIAVLFLVAGHMYRTNWGIGHSMKEILEAHRGPFTGEGHVGLYEILTTSWHAQLAINLALFGSLSIIVAHHMYAMPPYPYLATDYGTQLSLFTHHTWIGGFCIVGAGAHAAIFMVRDYDPTNNYNNLLDRVIRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVFAQWIQNTHFLAPQLTAPNALAATSLTWGGDLVAVGGKVAMMPISLGTSDFMVHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSLSIVIFHFSWKMQSDVWGTVTASGVSHITGGNFAQSANTINGWLRDFLWAQSSQVIQSYGSALSAYGLIFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPRALSITQGRAVGVAHYLLGGIATTWSFFLARIISVG

Entity 8 polymer

description	Photosystem I P700 chlorophyll a apoprotein A2
formula_weight	81982.0 kDa
ec_number	1.97.1.12
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

TKLFPKFSQGLAQDPTTRRIWYGLAMAHDFESHDGMTEENLYQKIFASHFGQLSIIFLWTSGNLFHVAWQGNFEQWVTDPVHIRPIAHAIWDPHFGQPAVEAFTRGGASGPVNISTSGVYQWWYTIGMRTNQDLYVGSVFLALVSAIFLFAGWLHLQPNFQPSLSWFKDAESRLNHHLSGLFGVSSLAWTGHLVHVAIPESRGQHVGWDNFLSVLPHPQGLTPFFTGNWAAYAQSPDTASHVFGTAQGSGQAILTFLGGFHPQTQSLWLTDMAHHHLAIAVIFIVAGHMYRTNFGIGHRMQAILEAHTPPSGSLGAGHKGLFDTVNNSLHFQLGLALASVGTITSLVAQHMYSLPPYAFQAIDFTTQAALYTHHQYIAGFIMCGAFAHGAIFFIRDYDPEQNKGNVLARMLDHKEALISHLSWVSLFLGFHTLGLYVHNDVMQAFGTPEKQILIEPVFAQWIQAAHGKALYGFDFLLSSKTSAAFANGQSLWLPGWLDAINNNQNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAYDAFYLAVFWMLNTIGWVTFYWHWKHLTLWQGNVAQFDESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWTFLFGHLIYATGFMFLISWRGYWQELIETLVWAHEKTPLANLVYWKDKPVALSIVQARLVGLAHFSVGYIFTYAAFLIASTSGRFG

Entity 9 polymer

description	Photosystem I iron-sulfur center
formula_weight	8738.1 kDa
ec_number	1.97.1.12
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

AHIVKIYDTCIGCTQCVRACPLDVLEMVPWDGCKASQMASAPRTEDCVGCKRCETACPTDFLSVRVYLGSESTRSMGLSY

Entity 10 polymer

description	Photosystem I reaction center subunit II, chloroplastic
formula_weight	16123.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

WTVPTLNPDTPSPIFGGSTGGLLRKAQTEEFYVITWEAKKEQIFEMPTGGAAIMRQGPNLLKFGKKEQCLALTTQLRNKFKLTPCFYRVFPDGKVQYLHPADGVYPEKVNAGRVGANQNMRRIGQNVNPIKVKFSGRMMSPAEI

Entity 11 polymer

description	Photosystem I reaction center subunit IV, chloroplastic
formula_weight	7151.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

EVGPKRGSLVKILRPESYWFNQVGKVVSVDQSGVRYPVVVRFENQNYAGVTTNNYALDEVVAAK

Entity 12 polymer

description	Photosystem I reaction center subunit VIII
formula_weight	3970.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

PFVPPSWAPSVFVPLTGLVLPAIAMATLFVYIEKEAP

Entity 13 polymer

description	Photosystem I reaction center subunit IX
formula_weight	4629.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

XMKDFTTYLSTAPVIATIWFTFTAGLLIEINRYFPDPLVFS

Entity 14 polymer

description	Photosystem I reaction center subunit psaK, chloroplastic
formula_weight	8316.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

GFIGSSTNLIMVASTTATLAAARFGLAPTVKKNTTAGLKLVDSKNSAGVISNDPAGFTIVDVLAMGAAGHGLGVGIVLGLKGIGAL

Entity 15 polymer

description	Chlorophyll a-b binding protein, chloroplastic
formula_weight	20368.0 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Z,1

KAGNWLPGSDAPAWLPDDLPGNYGFDPLSLGKEPASLKRFTESEVIHGRWAMLGVAGSLAVELLGYGNWYDAPLWAVNGGKATWFGIEVPFDLNALLAFEFVAMAAAEGQRGDAGGVVYPGGAFDPLGFAKDSSKSGELKLKEIKNGRLAMVAFLGFVAQHAATGKGPIAALGEHLANPWGANFATNGISVPFF

Entity 16 polymer

description	Photosystem I reaction center subunit III, chloroplastic
formula_weight	17957.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

DIAGLTPCSESKAYAKLEKKELKTLEKRLKQYEADSAPAVALKATMERTKARFANYAKAGLLCGNDGLPHLIADPGLALKYGHAGEVFIPTFGFLYVAGYIGYVGRQYLIAVKGEAKPTDKEIIIDVPLATKLAWQGAGWPLAAVQELQRGTLLEKEENITVSPR

Entity 17 polymer

description	Photosystem I reaction center subunit V, chloroplastic
formula_weight	9958.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

LDPQIVISGSTAAFLAIGRFVFLGYQRREANFDSTVGPKTTGATYFDDLQKNSTIFATNDPAGFNIIDVAGWGALGHAVGFAVLAINSLQGANLS

Entity 18 polymer

description	Chains: L
formula_weight	12744.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

GMLETPVTSAPIVATYLSNLPAYRTGVAPVLRGVEIGLAHGFLLAGPFIKLGPLRNVPETAEIAGSLSAAGLVLILALCLSIYGSAQFQSARDPLFSADGWSEFAAGFLVGGEAGVAWAYVCTQ

Entity 19 non-polymer

description	CHLOROPHYLL A
formula_weight	893.5 kDa
src_method	syn
entity_count	188

Entity 20 non-polymer

description	CHLOROPHYLL B
formula_weight	907.5 kDa
src_method	syn
entity_count	28

Entity 21 non-polymer

description	BETA-CAROTENE
formula_weight	536.9 kDa
src_method	syn
entity_count	27

Entity 22 non-polymer

description	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
formula_weight	568.9 kDa
src_method	syn
entity_count	16

Entity 23 non-polymer

description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
formula_weight	787.2 kDa
src_method	syn
entity_count	12

Entity 24 non-polymer

description	DODECYL-ALPHA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	27

Entity 25 non-polymer

description	;(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 ;
formula_weight	600.9 kDa
src_method	syn
entity_count	7

Entity 26 non-polymer

description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
formula_weight	723.0 kDa
src_method	syn
entity_count	14

Entity 27 non-polymer

description	;(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL ;
formula_weight	600.9 kDa
src_method	syn
entity_count	2

Entity 28 non-polymer

description	CHLOROPHYLL A ISOMER
formula_weight	893.5 kDa
src_method	syn
entity_count	1

Entity 29 non-polymer

description	PHYLLOQUINONE
formula_weight	450.7 kDa
src_method	syn
entity_count	2

Entity 30 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	3

Entity 31 non-polymer

description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
formula_weight	949.3 kDa
src_method	syn
entity_count	1

Entity 32 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1019

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.83 Å
resolution_method	—
num_particles	246159

fit	/app/data/saxs_computation/se/9se6/9se6.fit
pddf	/app/data/pr_computation/se/9se6/9se6.pr.out
profile	/app/data/saxs_computation/se/9se6/9se6.dat

Structure of Photosystem I from Chlamydomonas reinhardtii at 1.83 A resolution

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (32)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 polymer

Polymer

Entity 17 polymer

Polymer

Entity 18 polymer

Polymer

Entity 19 non-polymer

Entity 20 non-polymer

Entity 21 non-polymer

Entity 22 non-polymer

Entity 23 non-polymer

Entity 24 non-polymer

Entity 25 non-polymer

Entity 26 non-polymer

Entity 27 non-polymer

Entity 28 non-polymer

Entity 29 non-polymer

Entity 30 non-polymer

Entity 31 non-polymer

Entity 32 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)