MultifacetedProtDB - Bologna Biocomputing Group

Structure

PDB	Resolution (Å)	PDB name
1A15	2.2	SDF-1ALPHA
1QG7	2.0	STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA)
1SDF		SOLUTION STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), NMR, MINIMIZED AVERAGE STRUCTURE
1VMC		STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA)
2J7Z	1.95	Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha
2K01		Structure of a locked SDF1 dimer
2K03		Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21
2K04		Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
2K05		Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21
2KEC		Structure of SDF-1/CXCL12
2KED		Structure of SDF-1/CXCL12
2KEE		Structure of SDF-1/CXCL12
2KOL		Solution structure of human SDF1-alpha H25R
2N55		Structure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus
2NWG	2.07	Structure of CXCL12:heparin disaccharide complex
2SDF		SOLUTION NMR STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), 30 STRUCTURES
3GV3	1.6	CXCL12 (SDF) in trigonal space group
3HP3	2.2	Crystal structure of CXCL12
4LMQ	2.773	Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12
4UAI	1.9	Crystal structure of CXCL12 in complex with inhibitor
6SHR	1.745	X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRODUCED SDF1-A
7SK3	3.8	Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab
7SK4	3.3	Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab
7SK5	4.0	Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab
7SK6	4.0	Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ and an intracellular Fab
7SK7	3.3	Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab
7SK8	3.3	Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, an extracellular Fab, and an intracellular Fab

GO term

GO ontology	GO term	GO description
Biological Process	GO:0007186	G protein-coupled receptor signaling pathway
Biological Process	GO:0010818	T cell chemotaxis
Biological Process	GO:0008344	adult locomotory behavior
Biological Process	GO:0031100	animal organ regeneration
Biological Process	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide
Biological Process	GO:0007411	axon guidance
Biological Process	GO:0008015	blood circulation
Biological Process	GO:0007155	cell adhesion
Biological Process	GO:0060326	cell chemotaxis
Biological Process	GO:1990869	cellular response to chemokine
Biological Process	GO:0038146	chemokine (C-X-C motif) ligand 12 signaling pathway
Biological Process	GO:0070098	chemokine-mediated signaling pathway
Biological Process	GO:0006935	chemotaxis
Biological Process	GO:0006952	defense response
Biological Process	GO:0050966	detection of mechanical stimulus involved in sensory perception of pain
Biological Process	GO:0050965	detection of temperature stimulus involved in sensory perception of pain
Biological Process	GO:0006955	immune response
Biological Process	GO:0050930	induction of positive chemotaxis
Biological Process	GO:0033622	integrin activation
Biological Process	GO:0006874	intracellular calcium ion homeostasis
Biological Process	GO:0031640	killing of cells of another organism
Biological Process	GO:2000669	negative regulation of dendritic cell apoptotic process
Biological Process	GO:1902230	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
Biological Process	GO:1903237	negative regulation of leukocyte tethering or rolling
Biological Process	GO:0001764	neuron migration
Biological Process	GO:2000406	positive regulation of T cell migration
Biological Process	GO:0048842	positive regulation of axon extension involved in axon guidance
Biological Process	GO:0090280	positive regulation of calcium ion import
Biological Process	GO:0045785	positive regulation of cell adhesion
Biological Process	GO:0033603	positive regulation of dopamine secretion
Biological Process	GO:0001938	positive regulation of endothelial cell proliferation
Biological Process	GO:0090026	positive regulation of monocyte chemotaxis
Biological Process	GO:0045666	positive regulation of neuron differentiation
Biological Process	GO:0008064	regulation of actin polymerization or depolymerization
Biological Process	GO:0009408	response to heat
Biological Process	GO:0001666	response to hypoxia
Biological Process	GO:0043434	response to peptide hormone
Biological Process	GO:0009314	response to radiation
Biological Process	GO:1990478	response to ultrasound
Biological Process	GO:0009615	response to virus
Biological Process	GO:0007165	signal transduction
Biological Process	GO:0022029	telencephalon cell migration
Molecular Function	GO:0045236	CXCR chemokine receptor binding
Molecular Function	GO:0008009	chemokine activity
Molecular Function	GO:0042379	chemokine receptor binding
Molecular Function	GO:0008083	growth factor activity
Molecular Function	GO:0005178	integrin binding
Molecular Function	GO:0005102	signaling receptor binding
Cellular Component	GO:0062023	collagen-containing extracellular matrix
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0009897	external side of plasma membrane
Cellular Component	GO:0070062	extracellular exosome
Cellular Component	GO:0005576	extracellular region
Cellular Component	GO:0005634	nucleus

InterPro	InterPro name
IPR001811	Chemokine interleukin-8-like domain
IPR033899	CXC Chemokine domain
IPR036048	Chemokine interleukin-8-like superfamily
IPR039813	Stromal cell-derived factor 1

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-1251985	Nuclear signaling by ERBB4	Leaf	R-HSA-162582	Signal Transduction
R-HSA-376176	Signaling by ROBO receptors	Internal node	R-HSA-1266738	Developmental Biology
R-HSA-380108	Chemokine receptors bind chemokines	Leaf	R-HSA-162582	Signal Transduction
R-HSA-418594	G alpha (i) signalling events	Internal node	R-HSA-162582	Signal Transduction
R-HSA-9018519	Estrogen-dependent gene expression	Leaf	R-HSA-162582	Signal Transduction

Tissue	Cell type	Expression level	Reliability
testis	Leydig cells	Medium	Approved
testis	elongated or late spermatids	Low	Approved
testis	pachytene spermatocytes	Low	Approved
testis	preleptotene spermatocytes	Low	Approved
testis	round or early spermatids	Low	Approved
testis	spermatogonia cells	Medium	Approved

Summary of P48061

Gene: CXCL12, SDF1, SDF1A, SDF1B
Protein: Stromal cell-derived factor 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P48061

Gene: CXCL12, SDF1, SDF1A, SDF1B Protein: Stromal cell-derived factor 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: CXCL12, SDF1, SDF1A, SDF1B
Protein: Stromal cell-derived factor 1