8FR7

A hinge glycan regulates spike bending and impacts coronavirus infectivity

PDB DOI: https://doi.org/10.2210/pdb8FR7/pdb
EM Map EMD-22889: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human coronavirus NL63
Expression System: Chlorocebus pygerythrus
Mutation(s): No

Deposited: 2023-01-06 Released: 2023-10-04
Deposition Author(s): Pintilie, G., Wilson, E., Chmielewski, D., Schmid, M.F., Jin, J., Chen, M., Singharoy, A., Chiu, W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), National Institutes of Health/National Eye Institute (NIH/NEI), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7kip

Literature

A hinge glycan regulates spike bending and impacts coronavirus infectivity

Chmielewski, D., Wilson, E., Pintilie, G., Chen, M., Schmid, M.F., Wells, L., Jin, J., Singharoy, A., Chiu, W.

To be published.

Macromolecule Content

Total Structure Weight: 598.87 kDa
Atom Count: 39,808
Modelled Residue Count: 3,825
Deposited Residue Count: 4,068
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B [auth C], C [auth B]	1,356	Human coronavirus NL63	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for Q6Q1S2 (Human coronavirus NL63) Explore Q6Q1S2 Go to UniProtKB: Q6Q1S2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6Q1S2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AD [auth qA], BA [auth b], CB [auth 2], D, DB [auth 3], AD [auth qA], BA [auth b], CB [auth 2], D, DB [auth 3], EA [auth e], EB [auth 4], ED [auth uA], GD [auth wA], HB [auth 7], HC [auth XA], IA [auth i], ID [auth yA], KA [auth k], KB [auth AA], L, MA [auth m], MB [auth CA], NC [auth dA], OA [auth o], OC [auth eA], PB [auth FA], PC [auth fA], R, S, SC [auth iA], T, TB [auth JA], VB [auth LA], VC [auth lA], W, WA [auth w], XB [auth NA], XC [auth nA], Z, ZB [auth PA]	7		N-Glycosylation	Interactions Focus chain AD [auth qA] Focus chain BA [auth b] Focus chain CB [auth 2] Focus chain D Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain ED [auth uA] Focus chain GD [auth wA] Focus chain HB [auth 7] Focus chain HC [auth XA] Focus chain IA [auth i] Focus chain ID [auth yA] Focus chain KA [auth k] Focus chain KB [auth AA] Focus chain L Focus chain MA [auth m] Focus chain MB [auth CA] Focus chain NC [auth dA] Focus chain OA [auth o] Focus chain OC [auth eA] Focus chain PB [auth FA] Focus chain PC [auth fA] Focus chain R Focus chain S Focus chain SC [auth iA] Focus chain T Focus chain TB [auth JA] Focus chain VB [auth LA] Focus chain VC [auth lA] Focus chain W Focus chain WA [auth w] Focus chain XB [auth NA] Focus chain XC [auth nA] Focus chain Z Focus chain ZB [auth PA] Interactions & Density Focus chain AD [auth qA] Focus chain BA [auth b] Focus chain CB [auth 2] Focus chain D Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain ED [auth uA] Focus chain GD [auth wA] Focus chain HB [auth 7] Focus chain HC [auth XA] Focus chain IA [auth i] Focus chain ID [auth yA] Focus chain KA [auth k] Focus chain KB [auth AA] Focus chain L Focus chain MA [auth m] Focus chain MB [auth CA] Focus chain NC [auth dA] Focus chain OA [auth o] Focus chain OC [auth eA] Focus chain PB [auth FA] Focus chain PC [auth fA] Focus chain R Focus chain S Focus chain SC [auth iA] Focus chain T Focus chain TB [auth JA] Focus chain VB [auth LA] Focus chain VC [auth lA] Focus chain W Focus chain WA [auth w] Focus chain XB [auth NA] Focus chain XC [auth nA] Focus chain Z Focus chain ZB [auth PA]
Glycosylation Resources
GlyTouCan: G97423PY GlyCosmos: G97423PY GlyGen: G97423PY

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], AB [auth 0], AC [auth QA], BB [auth 1], BD [auth rA], AA [auth a], AB [auth 0], AC [auth QA], BB [auth 1], BD [auth rA], CA [auth c], CD [auth sA], DC [auth TA], DD [auth tA], E, EC [auth UA], FA [auth f], FB [auth 5], FC [auth VA], GA [auth g], GB [auth 6], GC [auth WA], H, HA [auth h], HD [auth xA], I, IB [auth 8], J, JB [auth 9], JC [auth ZA], K, KC [auth aA], LA [auth l], LB [auth BA], LC [auth bA], MC [auth cA], N, NB [auth DA], O, P, PA [auth p], Q, QB [auth GA], QC [auth gA], RB [auth HA], RC [auth hA], SA [auth s], SB [auth IA], TA [auth t], TC [auth jA], U, UA [auth u], UC [auth kA], V, VA [auth v], WB [auth MA], WC [auth mA], X, Y, YA [auth y], YC [auth oA], ZA [auth z]	7		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain AC [auth QA] Focus chain BB [auth 1] Focus chain BD [auth rA] Focus chain CA [auth c] Focus chain CD [auth sA] Focus chain DC [auth TA] Focus chain DD [auth tA] Focus chain E Focus chain EC [auth UA] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain FC [auth VA] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain GC [auth WA] Focus chain H Focus chain HA [auth h] Focus chain HD [auth xA] Focus chain I Focus chain IB [auth 8] Focus chain J Focus chain JB [auth 9] Focus chain JC [auth ZA] Focus chain K Focus chain KC [auth aA] Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain LC [auth bA] Focus chain MC [auth cA] Focus chain N Focus chain NB [auth DA] Focus chain O Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QB [auth GA] Focus chain QC [auth gA] Focus chain RB [auth HA] Focus chain RC [auth hA] Focus chain SA [auth s] Focus chain SB [auth IA] Focus chain TA [auth t] Focus chain TC [auth jA] Focus chain U Focus chain UA [auth u] Focus chain UC [auth kA] Focus chain V Focus chain VA [auth v] Focus chain WB [auth MA] Focus chain WC [auth mA] Focus chain X Focus chain Y Focus chain YA [auth y] Focus chain YC [auth oA] Focus chain ZA [auth z] Interactions & Density Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain AC [auth QA] Focus chain BB [auth 1] Focus chain BD [auth rA] Focus chain CA [auth c] Focus chain CD [auth sA] Focus chain DC [auth TA] Focus chain DD [auth tA] Focus chain E Focus chain EC [auth UA] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain FC [auth VA] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain GC [auth WA] Focus chain H Focus chain HA [auth h] Focus chain HD [auth xA] Focus chain I Focus chain IB [auth 8] Focus chain J Focus chain JB [auth 9] Focus chain JC [auth ZA] Focus chain K Focus chain KC [auth aA] Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain LC [auth bA] Focus chain MC [auth cA] Focus chain N Focus chain NB [auth DA] Focus chain O Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QB [auth GA] Focus chain QC [auth gA] Focus chain RB [auth HA] Focus chain RC [auth hA] Focus chain SA [auth s] Focus chain SB [auth IA] Focus chain TA [auth t] Focus chain TC [auth jA] Focus chain U Focus chain UA [auth u] Focus chain UC [auth kA] Focus chain V Focus chain VA [auth v] Focus chain WB [auth MA] Focus chain WC [auth mA] Focus chain X Focus chain Y Focus chain YA [auth y] Focus chain YC [auth oA] Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BC [auth RA], F, QA [auth q]	9		N-Glycosylation	Interactions Focus chain BC [auth RA] Focus chain F Focus chain QA [auth q] Interactions & Density Focus chain BC [auth RA] Focus chain F Focus chain QA [auth q]

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CC [auth SA], G, RA [auth r]	9		N-Glycosylation	Interactions Focus chain CC [auth SA] Focus chain G Focus chain RA [auth r] Interactions & Density Focus chain CC [auth SA] Focus chain G Focus chain RA [auth r]
Glycosylation Resources
GlyTouCan: G36191CD GlyCosmos: G36191CD GlyGen: G36191CD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	IC [auth YA], M, XA [auth x]	8		N-Glycosylation	Interactions Focus chain IC [auth YA] Focus chain M Focus chain XA [auth x] Interactions & Density Focus chain IC [auth YA] Focus chain M Focus chain XA [auth x]
Glycosylation Resources
GlyTouCan: G83582BK GlyCosmos: G83582BK GlyGen: G83582BK

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-L-fucopyranose-(1-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], OB [auth EA], ZC [auth pA]	12		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain OB [auth EA] Focus chain ZC [auth pA] Interactions & Density Focus chain DA [auth d] Focus chain OB [auth EA] Focus chain ZC [auth pA]

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FD [auth vA], JA [auth j], UB [auth KA]	5		N-Glycosylation	Interactions Focus chain FD [auth vA] Focus chain JA [auth j] Focus chain UB [auth KA] Interactions & Density Focus chain FD [auth vA] Focus chain JA [auth j] Focus chain UB [auth KA]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	JD [auth zA], NA [auth n], YB [auth OA]	2		O-Glycosylation	Interactions Focus chain JD [auth zA] Focus chain NA [auth n] Focus chain YB [auth OA] Interactions & Density Focus chain JD [auth zA] Focus chain NA [auth n] Focus chain YB [auth OA]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	KD [auth 0A], LD [auth 1A], MD [auth 2A], ND [auth 3A], OD [auth 4A], KD [auth 0A], LD [auth 1A], MD [auth 2A], ND [auth 3A], OD [auth 4A], PD [auth 5A], QD [auth 6A], RD [auth 7A]	7		N-Glycosylation	Interactions Focus chain KD [auth 0A] Focus chain LD [auth 1A] Focus chain MD [auth 2A] Focus chain ND [auth 3A] Focus chain OD [auth 4A] Focus chain PD [auth 5A] Focus chain QD [auth 6A] Focus chain RD [auth 7A] Interactions & Density Focus chain KD [auth 0A] Focus chain LD [auth 1A] Focus chain MD [auth 2A] Focus chain ND [auth 3A] Focus chain OD [auth 4A] Focus chain PD [auth 5A] Focus chain QD [auth 6A] Focus chain RD [auth 7A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01AI148382
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10OD021600
Department of Energy (DOE, United States)	United States	--
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	R01GM080139
National Science Foundation (NSF, United States)	United States	MCB-1942763
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	1R01NS119505-01A1
National Science Foundation (NSF, United States)	United States	ACI-1548562
Department of Energy (DOE, United States)	United States	DE-AC05-00OR22725