SAXSdb — 7ns6

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

Spike glycoprotein,Fibritin

Enterobacteria phage T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 2	Fu2 nanobody × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 46	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–1208； UniProt 1–1208 Author chain J； PDBConstruct 1–1208； UniProt 1–1208 Author chain K； PDBConstruct 1–1208； UniProt 1–1208 Author chain L； PDBConstruct 1–1208； UniProt 1–1208 Author chain M； PDBConstruct 1–1208； UniProt 1–1208 Author chain N； PDBConstruct 1–1208； UniProt 1–1208

Spike glycoprotein,Fibritin

Enterobacteria phage T4

UniProt P10104

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 2	Fu2 nanobody × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 46	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WAC_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1211–1237； UniProt 458–484 Author chain J； PDBConstruct 1211–1237； UniProt 458–484 Author chain K； PDBConstruct 1211–1237； UniProt 458–484 Author chain L； PDBConstruct 1211–1237； UniProt 458–484 Author chain M； PDBConstruct 1211–1237； UniProt 458–484 Author chain N； PDBConstruct 1211–1237； UniProt 458–484

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	7ns6
Deposition date deposition_date	2021-03-05
Structure title title	SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies
Keywords keywords	Nanobody, Spike, Complex, Dimer, VIRAL PROTEIN; VIRAL PROTEIN
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.

7ns6__assembly_1__model_1

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

Download this curve (.dat)

7ns6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ns6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	84.64 Å
Rg (electron density)	85.87 Å
Total Rg	85.86 Å
Atom count	55899
Residues	7109
Excluded volume	992050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ns6__assembly_1__model_1`	dodecameric （12）	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 (4)

Entity 1 Entity 1 polymer

Description description	Fu2 nanobody
Molecular weight formula_weight	15859.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,S,H,T,O,U
Atom count atom_count	55899

QVQLVESGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQAPGKEREGVSFITSSDGSTYYVDSVKGRFTISRDNAKNTVYLQMNSLTPEDTAIYYCAVGPSFSYTGSTYYRSELPWDYDYWGQGTQVTVSSGGLPETGGHHHHHH

Source Source

Source organism organism	Vicugna pacos
Common name common_name	alpaca
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Spike glycoprotein,Fibritin
Molecular weight formula_weight	142477.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K,M,J,L,N

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSPLGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

Source Source

Source organism organism	Enterobacteria phage T4
Common name common_name	Bacteriophage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 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	46

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	7ns6G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ns6H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ns6I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	7ns6J01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	7ns6K01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	7ns6L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	7ns6M01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	7ns6N01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	7ns6O01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ns6S01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ns6T01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ns6U01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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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	3.18 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	277372

SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies

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

Spike glycoprotein,Fibritin

State in the Current Structure

Other States of the Same Protein in the Database

Spike glycoprotein,Fibritin

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

7ns6__assembly_1__model_1

7ns6__assembly_1__model_1 | I(q)

7ns6__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)

SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies

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

Spike glycoprotein,Fibritin

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 glycoprotein,Fibritin

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

7ns6__assembly_1__model_1

7ns6__assembly_1__model_1 | I(q)

7ns6__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)