4NRL

Structure of hemagglutinin with F95Y mutation of influenza virus B/Lee/40

PDB DOI: https://doi.org/10.2210/pdb4NRL/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza B virus (B/Lee/1940)
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2013-11-26 Released: 2014-03-12
Deposition Author(s): Ni, F., Mbawuike, I.N., Kondrashkina, E., Wang, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.229
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 181.9 kDa
Atom Count: 12,583
Modelled Residue Count: 1,531
Deposited Residue Count: 1,584
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	346	Influenza B virus (B/Lee/1940)	Mutation(s): 1 Gene Names: HA
UniProt
Find proteins for P03460 (Influenza B virus (strain B/Lee/1940)) Explore P03460 Go to UniProtKB: P03460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03460
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	182	Influenza B virus (B/Lee/1940)	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P03460 (Influenza B virus (strain B/Lee/1940)) Explore P03460 Go to UniProtKB: P03460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03460
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G, L, Q	5		N/A	Interactions Focus chain G Focus chain L Focus chain Q Interactions & Density Focus chain G Focus chain L Focus chain Q
Glycosylation Resources
GlyTouCan: G79536OW GlyCosmos: G79536OW GlyGen: G79536OW

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	H, I, J, K, M H, I, J, K, M, O, P, R, S, T, U, V	2		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain J Focus chain K Focus chain M Focus chain O Focus chain P Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K Focus chain M Focus chain O Focus chain P Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	N	3		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
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 AA [auth E] SDF format, chain BA [auth F] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth D]	AA [auth E] BA [auth F] W [auth A] X [auth B] Y [auth C] AA [auth E], BA [auth F], W [auth A], X [auth B], Y [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.229
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.61	α = 90
b = 128.4	β = 90
c = 211.69	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASES	phasing
PHENIX	refinement
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-12
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary

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4NRL

Structure of hemagglutinin with F95Y mutation of influenza virus B/Lee/40

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)