8s0m

Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01

Method: X-RAY DIFFRACTION

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

Transmembrane protease serine 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Nanobody A01 × 1 Spike protein S1 × 1 （Q0ZME7） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PHOSPHATE ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Nanobody A01 × 1 Spike protein S1 × 1 （Q0ZME7） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PHOSPHATE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TMPS2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–386； UniProt 107–492 Author chain E； PDBConstruct 1–386； UniProt 107–492

Spike protein S1

Human coronavirus HKU1 (isolate N5)

UniProt Q0ZME7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Transmembrane protease serine 2 × 1 （O15393） Nanobody A01 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PHOSPHATE ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Transmembrane protease serine 2 × 1 （O15393） Nanobody A01 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PHOSPHATE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_CVHN5
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–366； UniProt 307–672 Author chain D； PDBConstruct 1–366； UniProt 307–672

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	8s0m
Deposition date deposition_date	2024-02-14
Structure title title	Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01
Keywords keywords	coronavirus receptor, VIRAL PROTEIN, PROTEASE, NANOBODY, VIRAL PROTEIN-RECEPTOR complex; VIRAL PROTEIN/RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

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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.

8s0m__assembly_1__model_1

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

Download this curve (.dat)

8s0m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8s0m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.18 Å
Rg (electron density)	37.63 Å
Total Rg	37.88 Å
Atom count	6419
Residues	818
Excluded volume	113260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8s0m__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8s0m__assembly_2__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	Transmembrane protease serine 2
Molecular weight formula_weight	43678.2 kDa
EC 编号 ec_number	3.4.21.122
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E
Atom count atom_count	12662

KFMGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSWHPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHSDACSSKAVVSLRCIACGVNLNSSRQSRIVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDAGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGGPFEDDDDK

Source Source

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

Entity 2 Entity 2 polymer

Description description	Nanobody A01
Molecular weight formula_weight	14961.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V

MAQVQLVESGGGLVQPGGSLRLSCVVSGFSLDYYAIGWFRQAPGKEREGVSCIGSSGDKTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAESALYSDCTEEQNPMLYDYWGQGTQVTVSSHHHHHH

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Spike protein S1
Molecular weight formula_weight	40835.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D

SGFTVKPVATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVNVTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSAICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINEEKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTEISTGVCVNYDLYGITGQGIFKEVSAVYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPC

Source Source

Source organism organism	Human coronavirus HKU1 (isolate N5)
NCBI taxonomy ID ncbi_taxonomy_id	443241
Host organism host_organism	Drosophila melanogaster

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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Unit-cell length a length_a	201.870 Å
Unit-cell length b length_b	201.870 Å
Unit-cell length c length_c	210.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.550 Å
Low-resolution limit resolution_low	24.970 Å
R factor r_factor	0.1943
R_work r_work	0.1929
R_free r_free	0.2213

Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01

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

Transmembrane protease serine 2

State in the Current Structure

Other States of the Same Protein in the Database

Spike protein S1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8s0m__assembly_1__model_1

8s0m__assembly_1__model_1 | I(q)

8s0m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (2)

Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01

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

Transmembrane protease serine 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Spike protein S1

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

8s0m__assembly_1__model_1

8s0m__assembly_1__model_1 | I(q)

8s0m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (2)