9tan

Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-quinone oxidoreductase subunit B

Escherichia coli BW25113

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	NADH-quinone oxidoreductase subunit C/D × 1 （P33599） NADH-quinone oxidoreductase subunit E × 1 （P0AFD1） NADH-quinone oxidoreductase subunit F × 1 （P31979） NADH-quinone oxidoreductase subunit G × 1 （P33602） NADH-quinone oxidoreductase subunit I × 1 （P0AFD6） IRON/SULFUR CLUSTER × 7 FE2/S2 (INORGANIC) CLUSTER × 2 CALCIUM ION × 4 FLAVIN MONONUCLEOTIDE × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUOB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–220； UniProt 1–220

NADH-quinone oxidoreductase subunit C/D

Escherichia coli BW25113

UniProt P33599

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	NADH-quinone oxidoreductase subunit B × 1 （P0AFC7） NADH-quinone oxidoreductase subunit E × 1 （P0AFD1） NADH-quinone oxidoreductase subunit F × 1 （P31979） NADH-quinone oxidoreductase subunit G × 1 （P33602） NADH-quinone oxidoreductase subunit I × 1 （P0AFD6） IRON/SULFUR CLUSTER × 7 FE2/S2 (INORGANIC) CLUSTER × 2 CALCIUM ION × 4 FLAVIN MONONUCLEOTIDE × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUOCD_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–600； UniProt 1–596

NADH-quinone oxidoreductase subunit E

Escherichia coli BW25113

UniProt P0AFD1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	NADH-quinone oxidoreductase subunit B × 1 （P0AFC7） NADH-quinone oxidoreductase subunit C/D × 1 （P33599） NADH-quinone oxidoreductase subunit F × 1 （P31979） NADH-quinone oxidoreductase subunit G × 1 （P33602） NADH-quinone oxidoreductase subunit I × 1 （P0AFD6） IRON/SULFUR CLUSTER × 7 FE2/S2 (INORGANIC) CLUSTER × 2 CALCIUM ION × 4 FLAVIN MONONUCLEOTIDE × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUOE_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–166； UniProt 1–166

NADH-quinone oxidoreductase subunit F

Escherichia coli BW25113

UniProt P31979

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	NADH-quinone oxidoreductase subunit B × 1 （P0AFC7） NADH-quinone oxidoreductase subunit C/D × 1 （P33599） NADH-quinone oxidoreductase subunit E × 1 （P0AFD1） NADH-quinone oxidoreductase subunit G × 1 （P33602） NADH-quinone oxidoreductase subunit I × 1 （P0AFD6） IRON/SULFUR CLUSTER × 7 FE2/S2 (INORGANIC) CLUSTER × 2 CALCIUM ION × 4 FLAVIN MONONUCLEOTIDE × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUOF_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 18–461； UniProt 2–445

NADH-quinone oxidoreductase subunit G

Escherichia coli BW25113

UniProt P33602

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	NADH-quinone oxidoreductase subunit B × 1 （P0AFC7） NADH-quinone oxidoreductase subunit C/D × 1 （P33599） NADH-quinone oxidoreductase subunit E × 1 （P0AFD1） NADH-quinone oxidoreductase subunit F × 1 （P31979） NADH-quinone oxidoreductase subunit I × 1 （P0AFD6） IRON/SULFUR CLUSTER × 7 FE2/S2 (INORGANIC) CLUSTER × 2 CALCIUM ION × 4 FLAVIN MONONUCLEOTIDE × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUOG_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain G； PDBConstruct 3–910； UniProt 1–908

NADH-quinone oxidoreductase subunit I

Escherichia coli BW25113

UniProt P0AFD6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	NADH-quinone oxidoreductase subunit B × 1 （P0AFC7） NADH-quinone oxidoreductase subunit C/D × 1 （P33599） NADH-quinone oxidoreductase subunit E × 1 （P0AFD1） NADH-quinone oxidoreductase subunit F × 1 （P31979） NADH-quinone oxidoreductase subunit G × 1 （P33602） IRON/SULFUR CLUSTER × 7 FE2/S2 (INORGANIC) CLUSTER × 2 CALCIUM ION × 4 FLAVIN MONONUCLEOTIDE × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUOI_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain I； PDBConstruct 1–180； UniProt 1–180

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9tan
Deposition date deposition_date	2025-11-18
Structure title title	Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG
Keywords keywords	;PROTON TRANSPORT, bioenergetics, Leigh's syndrome ;; PROTON TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9tan__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9tan__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9tan__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.37 Å
Rg (electron density)	43.47 Å
Total Rg	43.43 Å
Atom count	19382
Residues	2449
Excluded volume	344070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9tan__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	NADH-quinone oxidoreductase subunit B
Molecular weight formula_weight	25081.8 kDa
EC 编号 ec_number	7.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	19678

MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFGLSCCYVEMVTSFTAVHDVARFGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEPKWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPPRPEAYMQALMLLQESIGKERRPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI

Source Source

Source organism organism	Escherichia coli BW25113
NCBI taxonomy ID ncbi_taxonomy_id	679895
Host organism host_organism	Escherichia coli BW25113

Entity 2 Entity 2 polymer

Description description	NADH-quinone oxidoreductase subunit C/D
Molecular weight formula_weight	68780.5 kDa
EC 编号 ec_number	7.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MVNNMTDLTAQEPAWQTRDHLDDPVIGELRNRFGPDAFTVQATRTGVPVVWIKREQLLEVGDFLKKLPKPYVMLFDLHGMDERLRTHREGLPAADFSVFYHLISIDRNRDIMLKVALAENDLHVPTFTKLFPNANWYERETWDLFGITFDGHPNLRRIMMPQTWKGHPLRKDYPARATEFSPFELTKAKQDLEMEALTFKPEEWGMKRGTENEDFMFLNLGPNHPSAHGAFRIVLQLDGEEIVDCVPDIGYHHRGAEKMGERQSWHSYIPYTDRIEYLGGCVNEMPYVLAVEKLAGITVPDRVNVIRVMLSELFRINSHLLYISTFIQDVGAMTPVFFAFTDRQKIYDLVEAITGFRMHPAWFRIGGVAHDLPRGWDRLLREFLDWMPKRLASYEKAALQNTILKGRSQGVAAYGAKEALEWGTTGAGLRATGIDFDVRKARPYSGYENFDFEIPVGGGVSDCYTRVMLKVEELRQSLRILEQCLNNMPEGPFKADHPLTTPPPKERTLQHIETLITHFLQVSWGPVMPANESFQMIEATKGINSYYLTSDGSTMSYRTRVRTPSFAHLQQIPAAIRGSLVSDLIVYLGSIDFVMSDVDR

Source Source

Source organism organism	Escherichia coli BW25113
NCBI taxonomy ID ncbi_taxonomy_id	679895
Host organism host_organism	Escherichia coli BW25113

Entity 3 Entity 3 polymer

Description description	NADH-quinone oxidoreductase subunit E
Molecular weight formula_weight	18614.0 kDa
EC 编号 ec_number	7.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MHENQQPQTEAFELSAAEREAIEHEMHHYEDPRAASIEALKIVQKQRGWVPDGAIHAIADVLGIPASDVEGVATFYSQIFRQPVGRHVIRYCDSVVCHINGYQGIQAALEKKLNIKPGQTTFDGRFTLLPTCCLGNCDKGPNMMIDEDTHAHLTPEAIPELLERYK

Source Source

Source organism organism	Escherichia coli BW25113
NCBI taxonomy ID ncbi_taxonomy_id	679895
Host organism host_organism	Escherichia coli BW25113

Entity 4 Entity 4 polymer

Description description	NADH-quinone oxidoreductase subunit F
Molecular weight formula_weight	51208.4 kDa
EC 编号 ec_number	7.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MRGSHHHHHHTDPALRAKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW

Source Source

Source organism organism	Escherichia coli BW25113
NCBI taxonomy ID ncbi_taxonomy_id	679895
Host organism host_organism	Escherichia coli BW25113

Entity 5 Entity 5 polymer

Description description	NADH-quinone oxidoreductase subunit G
Molecular weight formula_weight	100663.6 kDa
EC 编号 ec_number	7.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MLMATIHVDGKEYEVNGADNLLEACLSLGLDIPYFCWHPALGSVGACRQCAVKQYQNAEDTRGRLVMSCMTPASDGTFISIDDEEAKQFRESVVEWLMTNHPHDCPVCEEGGNCHLQDMTVMTGHSFRRYRFTKRTHRNQDLGPFISHEMNRCIACYRCVRYYKDYADGTDLGVYGAHDNVYFGRPEDGTLESEFSGNLVEICPTGVFTDKTHSERYNRKWDMQFAPSICQQCSIGCNISPGERYGELRRIENRYNGTVNHYFLCDRGRFGYGYVNLKDRPRQPVQRRGDDFITLNAEQAMQGAADILRQSKKVIGIGSPRASVESNFALRELVGEENFYTGIAHGEQERLQLALKVLREGGIYTPALREIESYDAVLVLGEDVTQTGARVALAVRQAVKGKAREMAAAQKVADWQIAAILNIGQRAKHPLFVTNVDDTRLDDIAAWTYRAPVEDQARLGFAIAHALDNSAPAVDGIEPELQSKIDVIVQALAGAKKPLIISGTNAGSLEVIQAAANVAKALKGRGADVGITMIARSVNSMGLGIMGGGSLEEALTELETGRADAVVVLENDLHRHASAIRVNAALAKAPLVMVVDHQRTAIMENAHLVLSAASFAESDGTVINNEGRAQRFFQVYDPAYYDSKTVMLESWRWLHSLHSTLLSREVDWTQLDHVIDAVVAKIPELAGIKDAAPDATFRIRGQKLAREPHRYSGRTAMRANISVHEPRQPQDIDTMFTFSMEGNNQPTAHRSQVPFAWAPGWNSPQAWNKFQDEVGGKLRFGDPGVRLFETSENGLDYFTSVPARFQPQDGKWRIAPYYHLFGSDELSQRAPVFQSRMPQPYIKLNPADAAKLGVNAGTRVSFSYDGNTVTLPVEIAEGLTAGQVGLPMGMSGIAPVLAGAHLEDLKEAQQ

Source Source

Source organism organism	Escherichia coli BW25113
NCBI taxonomy ID ncbi_taxonomy_id	679895
Host organism host_organism	Escherichia coli BW25113

Entity 6 Entity 6 polymer

Description description	NADH-quinone oxidoreductase subunit I
Molecular weight formula_weight	20562.8 kDa
EC 编号 ec_number	7.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MTLKELLVGFGTQVRSIWMIGLHAFAKRETRMYPEEPVYLPPRYRGRIVLTRDPDGEERCVACNLCAVACPVGCISLQKAETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDFEMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDGKDKGEAENEAKPIDVKSLLP

Source Source

Source organism organism	Escherichia coli BW25113
NCBI taxonomy ID ncbi_taxonomy_id	679895
Host organism host_organism	Escherichia coli BW25113

Entity 7 Entity 7 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 8 Entity 8 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	296

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.59 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	86927

Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG

1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-quinone oxidoreductase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit C/D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit F

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit I

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9tan__assembly_1__model_1

9tan__assembly_1__model_1 | I(q)

9tan__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer