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- PDB-6nda: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CADMIUM -

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Basic information

Entry
Database: PDB / ID: 6nda
TitleRHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CADMIUM
Components
  • (Snaclec rhodocetin subunit ...) x 2
  • Integrin alpha-2
KeywordsCELL ADHESION/TOXIN / C-TYPE LECTIN / INTEGRIN / VENOM / COAGULATION / CELL ADHESION / CADMIUM / CELL ADHESION-TOXIN complex
Function / homology
Function and homology information


disruption of cell wall in another organism / collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid ...disruption of cell wall in another organism / collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid / oligosaccharide binding / CHL1 interactions / skin morphogenesis / Laminin interactions / mammary gland development / positive regulation of phagocytosis, engulfment / basal part of cell / positive regulation of smooth muscle contraction / collagen-activated signaling pathway / mesodermal cell differentiation / peptidoglycan binding / Platelet Adhesion to exposed collagen / hepatocyte differentiation / focal adhesion assembly / heparan sulfate proteoglycan binding / integrin complex / response to muscle activity / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cell adhesion mediated by integrin / MET activates PTK2 signaling / Syndecan interactions / positive regulation of epithelial cell migration / cell-substrate adhesion / positive regulation of smooth muscle cell migration / response to amine / positive regulation of collagen biosynthetic process / ECM proteoglycans / detection of mechanical stimulus involved in sensory perception of pain / Integrin cell surface interactions / laminin binding / axon terminus / collagen binding / positive regulation of cell adhesion / cell-matrix adhesion / extracellular matrix organization / positive regulation of translation / integrin-mediated signaling pathway / cellular response to estradiol stimulus / female pregnancy / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation / response to peptide hormone / cell-cell adhesion / cellular response to mechanical stimulus / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / integrin binding / signaling receptor activity / virus receptor activity / amyloid-beta binding / toxin activity / collagen-containing extracellular matrix / response to hypoxia / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / positive regulation of cell population proliferation / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
: / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. ...: / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / C-type lectin, conserved site / C-type lectin domain signature. / Integrin domain superfamily / Integrin alpha, N-terminal / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / AMMONIUM ION / Snaclec rhodocetin subunit gamma / Snaclec rhodocetin subunit delta / Integrin alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Calloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsStetefeld, J. / McDougall, M.D. / Loewen, P.C.
CitationJournal: To be published
Title: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CADMIUM
Authors: Stetefeld, J. / McDougall, M.D. / Loewen, P.C.
History
DepositionDec 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,72255
Polymers326,13118
Non-polymers2,59037
Water1267
1
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85010
Polymers54,3553
Non-polymers4947
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7188
Polymers54,3553
Non-polymers3635
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8149
Polymers54,3553
Non-polymers4596
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,83210
Polymers54,3553
Non-polymers4777
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-102 kcal/mol
Surface area19940 Å2
MethodPISA
5
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7188
Polymers54,3553
Non-polymers3635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-90 kcal/mol
Surface area20000 Å2
MethodPISA
6
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,78910
Polymers54,3553
Non-polymers4347
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-93 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.530, 130.530, 250.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Snaclec rhodocetin subunit ... , 2 types, 12 molecules ADGJMPBEHKNQ

#1: Protein
Snaclec rhodocetin subunit gamma


Mass: 15741.510 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW39
#2: Protein
Snaclec rhodocetin subunit delta


Mass: 14875.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW40

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Protein , 1 types, 6 molecules CFILOR

#3: Protein
Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / VLA-2 subunit alpha


Mass: 23737.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301

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Non-polymers , 6 types, 44 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M TRIS, 2.65 M Ammonium SULPHATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 27, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.15→130.53 Å / Num. obs: 67910 / % possible obs: 94 % / Redundancy: 4.4 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.121 / Rsym value: 0.107 / Net I/av σ(I): 6.6 / Net I/σ(I): 10.9 / Num. measured all: 296700
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.15-3.3240.4161.894840.2140.4720.41690.2
3.32-3.5240.2692.889020.140.3060.26989.4
3.52-3.763.90.1844.183340.0960.210.18489
3.76-4.073.70.1415.379260.0750.1610.14191.2
4.07-4.453.60.102776150.0560.1170.10295.4
4.45-4.983.80.0818.872380.0440.0930.08199.3
4.98-5.754.70.0868.264270.0440.0970.086100
5.75-7.045.90.0878.154160.0390.0960.087100
7.04-9.966.70.0512.642280.0210.0550.05100
9.96-92.2986.70.04214.823400.0170.0450.04299.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5THP

5thp


Resolution: 3.15→92.47 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.848 / WRfactor Rfree: 0.2425 / WRfactor Rwork: 0.1966 / FOM work R set: 0.7914 / SU B: 22.861 / SU ML: 0.381 / SU Rfree: 0.5145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 3402 5 %RANDOM
Rwork0.2119 ---
obs0.2149 64376 93.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.61 Å2 / Biso mean: 51.751 Å2 / Biso min: 3.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2--1.7 Å20 Å2
3----3.4 Å2
Refinement stepCycle: final / Resolution: 3.15→92.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21486 0 97 7 21590
Biso mean--69.44 22.96 -
Num. residues----2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01322128
X-RAY DIFFRACTIONr_bond_other_d0.0010.01819668
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.63729994
X-RAY DIFFRACTIONr_angle_other_deg1.1881.57945618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.70952646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93422.4631218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.939153708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.02615132
X-RAY DIFFRACTIONr_chiral_restr0.050.22766
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025028
LS refinement shellResolution: 3.15→3.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 253 -
Rwork0.303 4562 -
all-4815 -
obs--90.27 %

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