7EU3 | pdb_00007eu3

Chloroplast NDH complex

PDB DOI: https://doi.org/10.2210/pdb7EU3/pdb
EM Map EMD-31307: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Hordeum vulgare, Hordeum vulgare subsp. spontaneum
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2021-05-15 Released: 2021-12-29
Deposition Author(s): Wang, W.D., Shen, L., Tang, K., Han, G.Y., Zhang, X., Shen, J.R.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.

Shen, L., Tang, K., Wang, W., Wang, C., Wu, H., Mao, Z., An, S., Chang, S., Kuang, T., Shen, J.R., Han, G., Zhang, X.

(2022) Nature 601: 649-654

PubMed: 34879391 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-021-04277-6
Primary Citation Related Structures:
7EU3, 7EW6, 7EWK, 7F9O

PubMed Abstract:
The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET) ^1-3. The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.

Organizational Affiliation

Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content

Total Structure Weight: 707.89 kDa
Atom Count: 40,775
Modeled Residue Count: 5,399
Deposited Residue Count: 6,306
Unique protein chains: 25

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic	A	346	Hordeum vulgare	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for P92432 (Hordeum vulgare) Explore P92432 Go to UniProtKB: P92432
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P92432
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic	B	483	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for S4Z268 (Hordeum vulgare subsp. spontaneum) Explore S4Z268 Go to UniProtKB: S4Z268
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S4Z268
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic	C	117	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for S4Z1L1 (Hordeum vulgare subsp. spontaneum) Explore S4Z1L1 Go to UniProtKB: S4Z1L1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S4Z1L1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase chain 4, chloroplastic	D	499	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for S4Z8N2 (Hordeum vulgare subsp. spontaneum) Explore S4Z8N2 Go to UniProtKB: S4Z8N2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S4Z8N2
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic	E	100	Hordeum vulgare	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for P69378 (Hordeum vulgare) Explore P69378 Go to UniProtKB: P69378
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69378
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit F	F	777	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for Q32440 (Hordeum vulgare) Explore Q32440 Go to UniProtKB: Q32440
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32440
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic	G	176	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for A0A4Y5SEJ9 (Hordeum vulgare subsp. spontaneum) Explore A0A4Y5SEJ9 Go to UniProtKB: A0A4Y5SEJ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4Y5SEJ9
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit H, chloroplastic	H	383	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for S4Z272 (Hordeum vulgare subsp. spontaneum) Explore S4Z272 Go to UniProtKB: S4Z272
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S4Z272
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit I, chloroplastic	I	165	Hordeum vulgare	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for O98692 (Hordeum vulgare) Explore O98692 Go to UniProtKB: O98692
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O98692
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit J	J	159	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for Q7GT16 (Hordeum vulgare) Explore Q7GT16 Go to UniProtKB: Q7GT16
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7GT16
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit K, chloroplastic	K	245	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 7.1.1 Membrane Entity: Yes
UniProt
Find proteins for S4Z232 (Hordeum vulgare subsp. spontaneum) Explore S4Z232 Go to UniProtKB: S4Z232
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S4Z232
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit L	L	192	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2CUR7 (Hordeum vulgare subsp. vulgare) Explore F2CUR7 Go to UniProtKB: F2CUR7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2CUR7
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit M	M	213	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2D138 (Hordeum vulgare subsp. vulgare) Explore F2D138 Go to UniProtKB: F2D138
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2D138
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit N	N	233	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A3B6H0D5 (Triticum aestivum) Explore A0A3B6H0D5 Go to UniProtKB: A0A3B6H0D5
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UniProt Group	A0A3B6H0D5
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Unidentified stromal protein	O [auth T]	61	Hordeum vulgare subsp. spontaneum	Mutation(s): 0
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex L1	P [auth 1]	154	Hordeum vulgare subsp. spontaneum	Mutation(s): 0
UniProt
Find proteins for A0A8I6Y1Z8 (Hordeum vulgare subsp. vulgare) Explore A0A8I6Y1Z8 Go to UniProtKB: A0A8I6Y1Z8
Entity Groups
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UniProt Group	A0A8I6Y1Z8
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex L2	Q [auth 2]	216	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2CTW7 (Hordeum vulgare subsp. vulgare) Explore F2CTW7 Go to UniProtKB: F2CTW7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2CTW7
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex L3	R [auth 3]	227	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A8I6XER5 (Hordeum vulgare subsp. vulgare) Explore A0A8I6XER5 Go to UniProtKB: A0A8I6XER5
Entity Groups
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UniProt Group	A0A8I6XER5
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex L4	S [auth 4]	130	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 5.2.1.8
UniProt
Find proteins for A0A8I6YM48 (Hordeum vulgare subsp. vulgare) Explore A0A8I6YM48 Go to UniProtKB: A0A8I6YM48
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UniProt Group	A0A8I6YM48
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex L5	T [auth 5]	243	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 EC: 5.2.1.8
UniProt
Find proteins for F2CTD7 (Hordeum vulgare subsp. vulgare) Explore F2CTD7 Go to UniProtKB: F2CTD7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2CTD7
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex B1	U [auth 6]	469	Hordeum vulgare subsp. spontaneum	Mutation(s): 0
UniProt
Find proteins for F2D3G1 (Hordeum vulgare subsp. vulgare) Explore F2D3G1 Go to UniProtKB: F2D3G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2D3G1
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex B2	V [auth 7]	361	Hordeum vulgare subsp. spontaneum	Mutation(s): 0
UniProt
Find proteins for F2D932 (Hordeum vulgare subsp. vulgare) Explore F2D932 Go to UniProtKB: F2D932
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2D932
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex B3	W [auth 8]	119	Hordeum vulgare subsp. spontaneum	Mutation(s): 0
UniProt
Find proteins for F2DD79 (Hordeum vulgare subsp. vulgare) Explore F2DD79 Go to UniProtKB: F2DD79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2DD79
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex B4	X [auth 9]	83	Hordeum vulgare subsp. spontaneum	Mutation(s): 0
UniProt
Find proteins for F2CPQ4 (Hordeum vulgare subsp. vulgare) Explore F2CPQ4 Go to UniProtKB: F2CPQ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2CPQ4
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic NDH subunit of subcomplex B5	Y [auth 0]	155	Hordeum vulgare subsp. spontaneum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2DWH9 (Hordeum vulgare subsp. vulgare) Explore F2DWH9 Go to UniProtKB: F2DWH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2DWH9
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SQD Query on SQD Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F]	BA [auth F], CA [auth F]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C₄₁ H₇₈ O₁₂ S RVUUQPKXGDTQPG-JUDHQOGESA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F]
LHG Query on LHG Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain Z [auth D] Interactions & Density Focus chain Z [auth D]
BCR Query on BCR Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain AA [auth F]	AA [auth F]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain AA [auth F] Interactions & Density Focus chain AA [auth F]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth 8] MOL2 format, chain DA [auth 8] mmCIF format, chain DA [auth 8]	DA [auth 8]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain DA [auth 8] Interactions & Density Focus chain DA [auth 8]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK Query on UNK	O [auth T]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	QYZDY-SSW-SMC003

Revision History (Full details and data files)

Version 1.0: 2021-12-29
Type: Initial release
Version 1.1: 2022-02-09
Changes: Database references
Version 1.2: 2024-11-06
Changes: Data collection, Structure summary
Version 1.3: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations, Structure summary

7EU3 | pdb_00007eu3

Chloroplast NDH complex

Literature

Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

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Entity ID: 15

Sequence Annotations

Entity ID: 16

UniProt

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Sequence Annotations

Entity ID: 17

UniProt

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Sequence Annotations

Entity ID: 18

UniProt

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Sequence Annotations

Entity ID: 19

UniProt

Entity Groups

Sequence Annotations