6ENY

Structure of the human PLC editing module

PDB DOI: https://doi.org/10.2210/pdb6ENY/pdb
EM Map EMD-3906: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2017-10-07 Released: 2017-11-29
Deposition Author(s): Trowitzsch, S., Januliene, D., Blees, A., Moeller, A., Tampe, R.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.80 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: 197.81 kDa
Atom Count: 7,778
Modelled Residue Count: 1,563
Deposited Residue Count: 1,749
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	A [auth B]	99	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tapasin	B [auth C]	428	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O15533 (Homo sapiens) Explore O15533 Go to UniProtKB: O15533
PHAROS: O15533 GTEx: ENSG00000231925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15533
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase A3	C [auth D]	481	Homo sapiens	Mutation(s): 0 EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P30101 (Homo sapiens) Explore P30101 Go to UniProtKB: P30101
PHAROS: P30101 GTEx: ENSG00000167004
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30101
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-3 alpha chain	D [auth F]	341	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439
PHAROS: P04439 GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04439
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Calreticulin	E [auth G]	400	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P27797 (Homo sapiens) Explore P27797 Go to UniProtKB: P27797
PHAROS: P27797 GTEx: ENSG00000179218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27797
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth A]	2		N/A	Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	G [auth E]	4	N/A	N/A	Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 5.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	FREALIGN	X
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB 807
German Research Foundation	Germany	GRK 1986

Revision History (Full details and data files)

Version 1.0: 2017-11-29
Type: Initial release
Version 1.1: 2017-12-06
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary