7AKK | pdb_00007akk

Structure of a complement factor-receptor complex

PDB DOI: https://doi.org/10.2210/pdb7AKK/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-10-01 Released: 2022-04-13
Deposition Author(s): Fernandez, F.J., Santos-Lopez, J., Martinez-Barricarte, R., Querol-Garcia, J., Navas-Yuste, S., Savko, M., Shepard, W.E., Rodriguez de Cordoba, S., Vega, M.C.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, Spanish Ministry of Economy and Competitiveness, Other government, Spanish National Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of iC3b-CR3 alpha I reveals a modular recognition of the main opsonin iC3b by the CR3 integrin receptor

Fernandez, F.J., Santos-Lopez, J., Martinez-Barricarte, R., Querol-Garcia, J., Martin-Merinero, H., Navas-Yuste, S., Savko, M., Shepard, W.E., Rodriguez de Cordoba, S., Vega, M.C.

(2022) Nat Commun 13: 1955

DOI: https://doi.org/10.1038/s41467-022-29580-2

Macromolecule Content

Total Structure Weight: 393.32 kDa
Atom Count: 24,012
Modeled Residue Count: 3,006
Deposited Residue Count: 3,476
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3 beta chain	A [auth B], D [auth C]	645	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024 Go to UniProtKB: P01024
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01024
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth B] Focus chain D [auth C]	Go to GlyGen: P01024-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3b alpha' chain	B [auth A], E	898	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024 Go to UniProtKB: P01024
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01024
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E	Go to GlyGen: P01024-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-M	C [auth D], F [auth H]	195	Homo sapiens	Mutation(s): 2 Gene Names: ITGAM, CD11B, CR3A
UniProt & NIH Common Fund Data Resources
Find proteins for P11215 (Homo sapiens) Explore P11215 Go to UniProtKB: P11215
PHAROS: P11215 GTEx: ENSG00000169896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11215
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth I]	3	N/A	N-Glycosylation	Interactions Focus chain G [auth I] Interactions & Density Focus chain G [auth I]
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth J]	4	N/A	N-Glycosylation	Interactions Focus chain H [auth J] Interactions & Density Focus chain H [auth J]
Glycosylation Resources
GlyTouCan: G26644CA GlyCosmos: G26644CA GlyGen: G26644CA

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth E] MOL2 format, chain N [auth E] mmCIF format, chain N [auth E]	N [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth E] Interactions & Density Focus chain N [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain O [auth E] SDF format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth E] MOL2 format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth E] mmCIF format, chain I [auth B]	I [auth B], L [auth C], O [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth E] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth E]
K Query on K Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A]	J [auth A], M [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Interactions & Density Focus chain J [auth A] Focus chain M [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain K [auth D] MOL2 format, chain P [auth H] MOL2 format, chain K [auth D] mmCIF format, chain P [auth H] mmCIF format, chain K [auth D]	K [auth D], P [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain P [auth H] Interactions & Density Focus chain K [auth D] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.29	α = 90
b = 150.73	β = 92.8
c = 111.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-13

Deposition Author(s):

Fernandez, F.J.

Santos-Lopez, J.

Martinez-Barricarte, R.

Rodriguez de Cordoba, S.

Vega, M.C.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	RTI2018-102242-B-I00
Spanish Ministry of Economy and Competitiveness	Spain	SAF2015-72961-EXP
Spanish Ministry of Economy and Competitiveness	Spain	SAF2015-66287-R
Other government	Spain	S2017/BMD-3673
Spanish National Research Council	Spain	PIE-201620E064