6NB4

MERS-CoV S complex with human neutralizing LCA60 antibody Fab fragment (state 2)

PDB DOI: https://doi.org/10.2210/pdb6NB4/pdb
EM Map EMD-0402: EMDB EMDataResource

Classification: VIRUS
Organism(s): Middle East respiratory syndrome-related coronavirus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-12-06 Released: 2019-02-06
Deposition Author(s): Walls, A.C., Xiong, X., Park, Y.J., Tortorici, M.A., Snijder, S., Quispe, J., Cameroni, E., Gopal, R., Mian, D., Lanzavecchia, A., Zambon, M., Rey, F.A., Corti, D., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 495.35 kDa
Atom Count: 26,681
Modelled Residue Count: 3,315
Deposited Residue Count: 4,313
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,359	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for A0A140AYW5 (Middle East respiratory syndrome-related coronavirus) Explore A0A140AYW5 Go to UniProtKB: A0A140AYW5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A140AYW5
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LCA60 heavy chain	D [auth H]	127	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LCA60 light chain	E [auth L]	109	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], F [auth D], GA [auth g], H [auth F], HA [auth h], I [auth G], JA [auth j], K [auth J], L [auth K], LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, S, T, V, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain F [auth D] Focus chain GA [auth g] Focus chain H [auth F] Focus chain HA [auth h] Focus chain I [auth G] Focus chain JA [auth j] Focus chain K [auth J] Focus chain L [auth K] Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain S Focus chain T Focus chain V Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain F [auth D] Focus chain GA [auth g] Focus chain H [auth F] Focus chain HA [auth h] Focus chain I [auth G] Focus chain JA [auth j] Focus chain K [auth J] Focus chain L [auth K] Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain S Focus chain T Focus chain V Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	G [auth E], IA [auth i], J [auth I], QA [auth q], R, G [auth E], IA [auth i], J [auth I], QA [auth q], R, W	5		N-Glycosylation	Interactions Focus chain G [auth E] Focus chain IA [auth i] Focus chain J [auth I] Focus chain QA [auth q] Focus chain R Focus chain W Interactions & Density Focus chain G [auth E] Focus chain IA [auth i] Focus chain J [auth I] Focus chain QA [auth q] Focus chain R Focus chain W
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	U	6		N-Glycosylation	Interactions Focus chain U Interactions & Density Focus chain U
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	FA [auth f], X	4		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain X Interactions & Density Focus chain FA [auth f] Focus chain X
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	KA [auth k], Y	3		N-Glycosylation	Interactions Focus chain KA [auth k] Focus chain Y Interactions & Density Focus chain KA [auth k] Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain ZA [auth C] SDF format, chain TA [auth A] SDF format, chain YA [auth C] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain TA [auth A] MOL2 format, chain YA [auth C]	RA [auth A] SA [auth A] TA [auth A] UA [auth A] VA [auth B] RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth B], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta
RECONSTRUCTION	RELION	3.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM120553

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 1.1: 2019-02-20
Changes: Data collection, Database references
Version 1.2: 2019-03-06
Changes: Data collection, Database references
Version 1.3: 2020-01-08
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

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6NB4

MERS-CoV S complex with human neutralizing LCA60 antibody Fab fragment (state 2)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)