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- PDB-3hpn: Ligand recognition by A-class EPH receptors: crystal structures o... -

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Entry
Database: PDB / ID: 3hpn
TitleLigand recognition by A-class EPH receptors: crystal structures of the EPHA2 ligand-binding domain and the EPHA2/EPHRIN-A1 complex
ComponentsEphrin type-A receptor 2
KeywordsTRANSFERASE / Eph receptor tyrosine kinase / ephrin / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / tight junction / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / molecular function activator activity / negative regulation of angiogenesis / skeletal system development / protein localization to plasma membrane / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. ...Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsHimanen, J.P. / Goldgur, Y. / Miao, H. / Myshkin, E. / Guo, H. / Buck, M. / Nguyen, M. / Rajashankar, K.R. / Wang, B. / Nikolov, D.B.
CitationJournal: Embo Rep. / Year: 2009
Title: Ligand recognition by A-class Eph receptors: crystal structures of the EphA2 ligand-binding domain and the EphA2/ephrin-A1 complex.
Authors: Himanen, J.P. / Goldgur, Y. / Miao, H. / Myshkin, E. / Guo, H. / Buck, M. / Nguyen, M. / Rajashankar, K.R. / Wang, B. / Nikolov, D.B.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Mar 31, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-A receptor 2
B: Ephrin type-A receptor 2
C: Ephrin type-A receptor 2
D: Ephrin type-A receptor 2
E: Ephrin type-A receptor 2
F: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)119,4826
Polymers119,4826
Non-polymers00
Water18,5911032
1
A: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)19,9141
Polymers19,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)19,9141
Polymers19,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)19,9141
Polymers19,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)19,9141
Polymers19,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)19,9141
Polymers19,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)19,9141
Polymers19,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Ephrin type-A receptor 2
B: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)39,8272
Polymers39,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-13 kcal/mol
Surface area16340 Å2
MethodPISA, PQS
8
E: Ephrin type-A receptor 2
F: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)39,8272
Polymers39,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-13 kcal/mol
Surface area16310 Å2
MethodPISA, PQS
9
C: Ephrin type-A receptor 2
D: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)39,8272
Polymers39,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-12 kcal/mol
Surface area16300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.271, 91.187, 91.132
Angle α, β, γ (deg.)117.140, 97.270, 100.790
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 3 / Auth seq-ID: 1 - 174 / Label seq-ID: 1 - 174

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Ephrin type-A receptor 2 / Tyrosine-protein kinase receptor ECK / Epithelial cell kinase


Mass: 19913.592 Da / Num. of mol.: 6 / Fragment: UNP residues 28-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Plasmid: pBabe / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo Sapiens (human)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1032 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 4,000, 100 mM Tris, 100 mM Sodium Acetate, 3% ethylene glycol, pH 8.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 38120 / Num. obs: 36900 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.094 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.2 / % possible all: 80.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ETP

3etp


Resolution: 2.52→30 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.825 / Occupancy max: 1 / Occupancy min: 1 / SU B: 29.348 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3074 1856 5 %RANDOM
Rwork0.23249 ---
obs0.2362 35046 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 2.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.71 Å21.79 Å2
2--0.03 Å2-0.25 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.52→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8394 0 0 1032 9426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228610
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.94211664
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63251038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61723.803426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.822151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5221554
X-RAY DIFFRACTIONr_chiral_restr0.0870.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.091.55166
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.14828304
X-RAY DIFFRACTIONr_scbond_it0.40133444
X-RAY DIFFRACTIONr_scangle_it0.4594.53360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A696tight positional0.060.05
B696tight positional0.060.05
C696tight positional0.060.05
D696tight positional0.060.05
E696tight positional0.060.05
F696tight positional0.060.05
A703loose positional0.15
B703loose positional0.095
C703loose positional0.15
D703loose positional0.15
E703loose positional0.095
F703loose positional0.095
A696tight thermal0.020.5
B696tight thermal0.040.5
C696tight thermal0.030.5
D696tight thermal0.040.5
E696tight thermal0.040.5
F696tight thermal0.030.5
A703loose thermal0.0810
B703loose thermal0.0710
C703loose thermal0.0610
D703loose thermal0.0710
E703loose thermal0.0610
F703loose thermal0.0710
LS refinement shellResolution: 2.52→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 113 -
Rwork0.25 2181 -
obs--80.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0919-0.053-0.83471.00190.07851.59350.0054-0.0174-0.00130.0198-0.01010.08530.0635-0.01650.00470.10310.0741-0.05760.18110.04230.10962.617-55.85448.477
21.28110.0738-0.34470.78030.1241.6991-0.02420.06970.0345-0.0180.0143-0.0510.0023-0.0260.00990.11420.088-0.08260.1870.00890.11419.169-59.95714.506
31.5074-0.35130.3731.0732-0.32840.9054-0.0345-0.0321-0.00370.01580.02180.0010.0575-0.0470.01270.10070.0895-0.03940.17680.04060.09580.5280.2012.479
41.3987-0.22830.04291.5397-0.71391.1517-0.0015-0.0098-0.0866-0.00480.0451-0.0012-0.0243-0.0204-0.04360.1460.1097-0.05460.20680.04830.09737.905-26.95423.628
51.30350.53930.4331.07690.43051.0277-0.0575-0.02-0.0140.0080.04580.0245-0.0303-0.02790.01170.10440.0985-0.04390.18750.04070.09413.688-66.839-23.648
61.13630.38720.20462.53940.69681.1891-0.1389-0.24040.16420.02120.0464-0.0542-0.08430.04270.09250.13520.1402-0.11570.2476-0.03520.203410.342-35.61-9.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 174
2X-RAY DIFFRACTION2B1 - 174
3X-RAY DIFFRACTION3C1 - 174
4X-RAY DIFFRACTION4D1 - 174
5X-RAY DIFFRACTION5E1 - 174
6X-RAY DIFFRACTION6F1 - 174

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