9p0x

Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted)

Method: ELECTRON MICROSCOPY

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

Factor VII light chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Factor X light chain × 1 （P00742） Tissue factor,Maltose/maltodextrin-binding periplasmic protein × 1 （P0AEY0,P13726） Tissue factor pathway inhibitor × 1 （P10646） Human 10H10 antibody Fab heavy chain × 1 Human 10H10 antibody Fab light chain × 1 MAGNESIUM ION × 4 CALCIUM ION × 12 beta-D-glucopyranose × 1 alpha-L-fucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA7_HUMAN
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain V； PDBConstruct 1–142； UniProt 61–202 Author chain S； PDBConstruct 1–254； UniProt 213–466

Factor X light chain

Homo sapiens

UniProt P00742

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Factor VII light chain × 1 （P08709） Coagulation factor VII Heavy Chain × 1 （P08709） Tissue factor,Maltose/maltodextrin-binding periplasmic protein × 1 （P0AEY0,P13726） Tissue factor pathway inhibitor × 1 （P10646） Human 10H10 antibody Fab heavy chain × 1 Human 10H10 antibody Fab light chain × 1 MAGNESIUM ION × 4 CALCIUM ION × 12 beta-D-glucopyranose × 1 alpha-L-fucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA10_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 1–131； UniProt 41–171

Tissue factor,Maltose/maltodextrin-binding periplasmic protein

Escherichia coli

UniProt P0AEY0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Factor VII light chain × 1 （P08709） Factor X light chain × 1 （P00742） Coagulation factor VII Heavy Chain × 1 （P08709） Tissue factor pathway inhibitor × 1 （P10646） Human 10H10 antibody Fab heavy chain × 1 Human 10H10 antibody Fab light chain × 1 MAGNESIUM ION × 4 CALCIUM ION × 12 beta-D-glucopyranose × 1 alpha-L-fucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECO57
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain T； PDBConstruct 246–611； UniProt 27–392

Tissue factor,Maltose/maltodextrin-binding periplasmic protein

Escherichia coli

UniProt P13726

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Factor VII light chain × 1 （P08709） Factor X light chain × 1 （P00742） Coagulation factor VII Heavy Chain × 1 （P08709） Tissue factor pathway inhibitor × 1 （P10646） Human 10H10 antibody Fab heavy chain × 1 Human 10H10 antibody Fab light chain × 1 MAGNESIUM ION × 4 CALCIUM ION × 12 beta-D-glucopyranose × 1 alpha-L-fucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain T； PDBConstruct 1–239； UniProt 38–276

Tissue factor pathway inhibitor

Homo sapiens

UniProt P10646

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Factor VII light chain × 1 （P08709） Factor X light chain × 1 （P00742） Coagulation factor VII Heavy Chain × 1 （P08709） Tissue factor,Maltose/maltodextrin-binding periplasmic protein × 1 （P0AEY0,P13726） Human 10H10 antibody Fab heavy chain × 1 Human 10H10 antibody Fab light chain × 1 MAGNESIUM ION × 4 CALCIUM ION × 12 beta-D-glucopyranose × 1 alpha-L-fucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TFPI1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain K； PDBConstruct 1–68； UniProt 40–107

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	9p0x
Deposition date deposition_date	2025-06-07
Structure title title	Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted)
Keywords keywords	complex, nanodisc, blood clotting; BLOOD CLOTTING
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.

9p0x__assembly_1__model_1

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

Download this curve (.dat)

9p0x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9p0x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.43 Å
Rg (electron density)	39.93 Å
Total Rg	40.41 Å
Atom count	9723
Residues	1216
Excluded volume	171740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9p0x__assembly_1__model_1`	heptameric （7）	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	Factor VII light chain
Molecular weight formula_weight	16359.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V
Atom count atom_count	9725

ANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Factor X light chain
Molecular weight formula_weight	15309.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

ANSFLEEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGKCKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Coagulation factor VII Heavy Chain
Molecular weight formula_weight	28103.3 kDa
EC 编号 ec_number	3.4.21.21
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Tissue factor,Maltose/maltodextrin-binding periplasmic protein
Molecular weight formula_weight	67828.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECMGQEKGEFREIFYIIGAVVFVVIILVIILAISLHKGSGSGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQT

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Tissue factor pathway inhibitor
Molecular weight formula_weight	7979.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

TDTELPPLKLMHSFCAFKADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEECKKMCTRD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Human 10H10 antibody Fab heavy chain
Molecular weight formula_weight	23569.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVHLQQSGAELMKPGASVKISCKASGYTFITYWIEWVKQRPGHGLEWIGDILPGSGSTNYNENFKGKATFTADSSSNTAYMQLSSLTSEDSAVYYCARSGYYGNSGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Entity 7 Entity 7 polymer

Description description	Human 10H10 antibody Fab light chain
Molecular weight formula_weight	24196.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLSSGNQKNYLTWYQQIPGQPPKLLIYWASTRESGVPDRFTGSGSGTDFTLTINSVQAEDLAVYYCQNDYTYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSATDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	12

Entity 10 Entity 10 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	20107

Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted)

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

Factor VII light chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Factor X light chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tissue factor,Maltose/maltodextrin-binding periplasmic protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tissue factor,Maltose/maltodextrin-binding periplasmic protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tissue factor pathway inhibitor

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

9p0x__assembly_1__model_1

9p0x__assembly_1__model_1 | I(q)

9p0x__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

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

7. Citations (1)