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7n0i

Structure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoprotein

Severe acute respiratory syndrome coronavirus 2

UniProt P0DTC9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Single-domain antibody E2 × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Single-domain antibody E2 × 1 ACETATE ION × 1 MAGNESIUM ION × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Single-domain antibody E2 × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Single-domain antibody E2 × 1 ACETATE ION × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6m3m 6m3m 6m3m 6m3m 6yi3 7cdz 7cdz 7cdz 7cdz 7sd4 7uw3 7uw3

81 assemblies; showing the first 12

Homodimer
26ui 6wji 6wji 6wji 6wzo 6wzo 6wzq 6wzq 6yun 6zco 7c22 7c22

58 assemblies; showing the first 12

Homotetramer
6vyo 6wkp 7xx1 8iv3 8j6x

5 assemblies

Other homooligomers
7lux 7luz 7lv2

3 assemblies

Heteromeric or nucleic-acid complex
7acs 7act 7cr5 7kgo 7kgp 7kgq 7kgr 7kgs 7kgt 7lgd 7lgd 7n0i

75 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NCAP_SARS2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–96； UniProt 269–364 Author chain B； PDBConstruct 1–96； UniProt 269–364 Author chain C； PDBConstruct 1–96； UniProt 269–364 Author chain D； PDBConstruct 1–96； UniProt 269–364 Author chain E； PDBConstruct 1–96； UniProt 269–364 Author chain F； PDBConstruct 1–96； UniProt 269–364 Author chain G； PDBConstruct 1–96； UniProt 269–364 Author chain H； PDBConstruct 1–96； UniProt 269–364

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_id7n0i
Deposition date deposition_date2021-05-25
Structure title titleStructure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2
Keywords keywordsSARS-CoV-2, nanobody, nucleocapsid, VIRUS, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-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.

7n0i__assembly_1__model_1

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

Download this curve (.dat)

7n0i__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

7n0i__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）22.74 Å
Rg (electron density)21.99 Å
Total Rg22.78 Å
Atom count2578
Residues328
Excluded volume45194 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7n0i__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 7n0i__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 7n0i__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 7n0i__assembly_4__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 (5)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd7n0ia_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0ib_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0ic_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0id_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0ie_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0if_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0ig_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0ih_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.254 — Nucleocapsid protein dimerization domain
Superfamily Superfamily superfamilyd.254.1 — Nucleocapsid protein dimerization domain
Family Family familyd.254.1.2 — Coronavirus nucleocapsid protein
Domain ID domain_idd7n0ii1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd7n0ii2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd7n0ij1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd7n0ij2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd7n0ik1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd7n0ik2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd7n0il1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd7n0il2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id7n0iI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7n0iJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7n0iK01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7n0iL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (2)