Viral protein-Human protein complex

Macromolecule
Gene
Interacting molecule/ protein
Interacting gene
PDB ID
Title
Structure Title
Experimental Method
Resolution (Å)
PubMed ID
Structure
Spike glycoprotein
S, 2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
7A98
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
SARS-CoV-2 Spike Glycoprotein with 3 ACE2 Bound
Electron Microscopy
5.4
32942285
3D view
Spike glycoprotein
S, 2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
7A97
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
SARS-CoV-2 Spike Glycoprotein with 2 ACE2 Bound
Electron Microscopy
4.4
32942285
3D view
Spike glycoprotein
S, 2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
7A92
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Unmasked Refinement)
Electron Microscopy
4.2
32942285
3D view
Spike glycoprotein
S, 2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
7A91
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Electron Microscopy
3.6
32942285
3D view
Spike glycoprotein
S, 2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
7A94
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound
Electron Microscopy
3.9
32942285
3D view
Spike glycoprotein
S, 2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
7A96
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound and 1 RBD Erect in Anticlockwise Direction
Electron Microscopy
4.8
32942285
3D view
Spike glycoprotein
S, 2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
7A95
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound and 1 RBD Erect in Clockwise Direction
Electron Microscopy
4.3
32942285
3D view
nsp1
rep, 1a-1b
CCDC124-80S-eERF1 ribosome complex
~
6ZME
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex
Electron Microscopy
3
32680882
3D view
nsp1
rep, 1a-1b
40S ribosomal subunit complex
~
6ZLW
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit
Electron Microscopy
2.6
32680882
3D view
nsp1
rep, 1a-1b
human CCDC124-80S-EBP1 ribosome complex
~
6ZM7
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex
Electron Microscopy
2.7
32680882
3D view
nsp1
rep, 1a-1b
pre-40S-like ribosome complex
~
6ZMT
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex
Electron Microscopy
3
32680882
3D view
nsp1
rep, 1a-1b
pre-40S-like ribosome complex - state 2
~
6ZN5
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2
Electron Microscopy
3.2
32680882
3D view
nsp1
rep, 1a-1b
human LYAR-80S ribosome complex
~
6ZMI
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex
Electron Microscopy
2.6
32680882
3D view
nsp1
rep, 1a-1b
LYAR-80S-eEF1a ribosome complex
~
6ZMO
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex
Electron Microscopy
3.1
32680882
3D view
nsp1
rep, 1a-1b
40S complex
~
6ZOJ
SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
SARS-CoV-2-Nsp1-40S complex, composite map
Electron Microscopy
2.8
32908316
3D view
nsp1
rep, 1a-1b
40S complex
~
6ZOK
SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
SARS-CoV-2-Nsp1-40S complex, focused on body
Electron Microscopy
2.8
32908316
3D view
nsp1
rep, 1a-1b
human 43S preinitiation ribosome
~
6ZON
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
Electron Microscopy
3
32680882
3D view
Receptor binding domain
S,2
1.Sodium-dependent neutral amino acid transporter B(0)AT1 2.Angiotensin-converting enzyme 2
SLC6A19, B0AT1, ACE2, UNQ868/PRO1885
6M17
Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
The 2019-nCoV RBD/ACE2-B0AT1 complex
Electron Microscopy
2.9
32132184
3D view
Spike glycoprotein RBD
S,2
Angiotensin-converting enzyme 2
ACE2 UNQ868/PRO1885
6M0J
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
X-ray diffraction
2.45
32225176
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
6LZG
Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.
Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2
X-ray diffraction
2.5
32275855
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7DF4
Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM.
SARS-CoV-2 S-ACE2 complex
Electron Microscopy
3.8
33277323
3D view
Nsp1
rep, 1a-1b
40S ribosomal complex
RPSA, RPS3A, RPS28, RPS5, RPS9, RPS13, RPS15, RPS21
7JQB
Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.
SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
Electron Microscopy
2.7
33188728
3D view
Nsp1
rep, 1a-1b
40S ribosomal complex
RPSA, RPS3A, RPS28, RPS5, RPS9, RPS13, RPS15, RPS21
7JQC
Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.
SARS-CoV-2 Nsp1, CrPV IRES and rabbit 40S ribosome complex
Electron Microscopy
3.3
33188728
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2
7C8D
Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2.
Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
Electron Microscopy
3
33020722
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7CT5
Engineered trimeric ACE2 binds viral spike protein and locks it in "Three-up" conformation to potently inhibit SARS-CoV-2 infection.
S protein of SARS-CoV-2 in complex bound with T-ACE2
Electron Microscopy
4
33177651
3D view
Spike glycoprotein
S,2
Neuropilin-1
NRP1, NRP, VEGF165R
7JJC
Neuropilin-1 is a host factor for SARS-CoV-2 infection.
Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide
X-ray diffraction
2.36
33082294
3D view
Nsp1
40S ribosome
RPS17, RPS17L, RPS29, RPS3, OK/SW-cl.26, RPS5, RPS10, RPS12, RPS15, RIG, RPS16, RPS18, D6S218E, RPS19, RPS20, RPS25, RPS28, RPS27A, UBA80, UBCEP1, RACK1, GNB2L1, HLC7, PIG21, RPSA, LAMBR, LAMR1, RPS3A, FTE1, MFTL, RPS2, RPS4, RPS4X, CCG2, RPS4, SCAR, RPS6, OK/SW-cl.2, RPS7, RPS8, OK/SW-cl.83, RPS9, RPS11, RPS13, RPS14, PRO2640, RPS21, RPS15A, OK/SW-cl.82, RPS23, RPS24, RPS26, RPS27, MPS1, FAU, RPL41,
7K5I
SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism.
SARS-COV-2 nsp1 in complex with human 40S ribosome
Electron Microscopy
2.9
32995777
3D view
Orf9b
9b
Mitochondrial import receptor subunit TOM70
KIAA0719 TOMM70 TOMM70A
7KDT
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Human Tom70 in complex with SARS CoV2 Orf9b
Electron Microscopy
3.05
33060197
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KJ4
A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
SARS-CoV-2 Spike Glycoprotein with three ACE2 Bound
Electron Microscopy
3.4
32995768
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KJ2
A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
SARS-CoV-2 Spike Glycoprotein with one ACE2 Bound
Electron Microscopy
3.6
32995768
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KJ3
A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
SARS-CoV-2 Spike Glycoprotein with two ACE2 Bound
Electron Microscopy
3.7
32995768
3D view
Protein 3a
Apolipoprotein A-I
APOA1
7KJR
Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs.
Cryo-EM structure of SARS-CoV-2 ORF3a
Electron Microscopy
2.08
32587976
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KMS
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4
Electron Microscopy
3.64
33271067
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KMB
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4
Electron Microscopy
3.39
33271067
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KNE
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5
Electron Microscopy
3.85
33271067
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KNB
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 7.4
Electron Microscopy
3.93
33271067
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KNH
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cryo-EM Structure of Double ACE2-Bound SARS-CoV-2 Trimer Spike at pH 5.5
Electron Microscopy
3.74
33271067
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KNI
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cryo-EM structure of Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 5.5
Electron Microscopy
3.91
33271067
3D view
Spike glycoprotein
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
7KMZ
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4
Electron Microscopy
3.62
33271067
3D view
SARS-CoV-2 chimeric RBD
S,2
Angiotensin-converting enzyme 2
ACE2, UNQ868/PRO1885
6VW1
Structural basis of receptor recognition by SARS-CoV-2.
Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2
X-ray diffraction
2.68
32225175
3D view