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- PDB-3i85: The Crystal Structure of Human EMMPRIN N-terminal Domain 1 -

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Basic information

Entry
Database: PDB / ID: 3i85
TitleThe Crystal Structure of Human EMMPRIN N-terminal Domain 1
ComponentsCervical EMMPRIN
KeywordsCELL ADHESION / EMMPRIN / CD147 / dimerization / beta-strand swapping
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / lateral plasma membrane / Integrin cell surface interactions / response to cAMP / Degradation of the extracellular matrix / photoreceptor inner segment / embryo implantation / positive regulation of endothelial cell migration / neutrophil chemotaxis / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, J. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2009
Title: Structure of the EMMPRIN N-terminal domain 1: Dimerization via beta-strand swapping.
Authors: Luo, J. / Teplyakov, A. / Obmolova, G. / Malia, T. / Wu, S.J. / Beil, E. / Baker, A. / Swencki-Underwood, B. / Zhao, Y. / Sprenkle, J. / Dixon, K. / Sweet, R. / Gilliland, G.L.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 31, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 27, 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: Cervical EMMPRIN
B: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)21,1172
Polymers21,1172
Non-polymers00
Water21612
1
A: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)10,5591
Polymers10,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)10,5591
Polymers10,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.480, 83.480, 49.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 25:44 or resseq 49:94 ) and backbone
211chain B and (resseq 25:44 or resseq 49:94 ) and backbone
112chain A and (resseq 95:102 )
212chain B and (resseq 95:102 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.293423, 0.758542, 0.581822), (0.799755, -0.5282, 0.285302), (0.523732, 0.381601, -0.761633)55.662899, -84.221199, -10.705
3given(0.273648, 0.860403, 0.429911), (0.782433, -0.459087, 0.420759), (0.559388, 0.221237, -0.798836)59.435699, -81.3843, -17.5993

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Components

#1: Protein Cervical EMMPRIN


Mass: 10558.675 Da / Num. of mol.: 2 / Mutation: A19D, N44D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hEMMPRIN, BSG, hCG_20562 / Plasmid: pCEP4 / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo Sapiens (human) / References: UniProt: Q54A51, UniProt: P35613*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.2 M sodium formate, 3% MPD, 0.1 M sodium citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 7, 2007 / Details: Osmic VariMax Confocal
RadiationMonochromator: Osmic VariMax Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→42 Å / Num. all: 7149 / Num. obs: 7149 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.4 % / Biso Wilson estimate: 95.5 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.591 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 3B5H

3b5h


Resolution: 2.5→29.237 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.98 / σ(F): 1.34 / Phase error: 35.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 335 4.71 %
Rwork0.2273 --
obs0.2287 7117 99.69 %
all-7117 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.124 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 90.571 Å2
Baniso -1Baniso -2Baniso -3
1--5.601 Å20 Å20 Å2
2---5.601 Å20 Å2
3---11.202 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 12 1241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091253
X-RAY DIFFRACTIONf_angle_d1.3241696
X-RAY DIFFRACTIONf_dihedral_angle_d18.637438
X-RAY DIFFRACTIONf_chiral_restr0.101199
X-RAY DIFFRACTIONf_plane_restr0.006214
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A268X-RAY DIFFRACTIONPOSITIONAL
12B268X-RAY DIFFRACTIONPOSITIONAL0.068
21A59X-RAY DIFFRACTIONPOSITIONAL
22B59X-RAY DIFFRACTIONPOSITIONAL0.091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.14960.39441610.27663340X-RAY DIFFRACTION100
3.1496-29.23950.22931740.21283442X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.58452.30242.88486.13610.59236.55070.1787-0.29920.42180.2596-0.34790.59210.1287-0.23090.23450.3509-0.05680.00390.3689-0.05620.39823.4296-29.92896.6966
20.3274-1.3356-0.18214.79880.68675.5898-0.40380.2715-0.6876-0.349-0.5688-1.7738-0.14420.01160.37170.2556-0.04630.41050.4241-0.04190.7674
34.91821.79231.87390.3487-1.38813.60920.041-0.01120.20880.00030.3821-0.23181.3301-0.2757-0.60610.876-0.1837-0.45380.61470.08920.8182
45.19071.90141.05562.0897-0.37915.3089-0.1157-0.1815-0.7891-0.21890.2262-0.70620.5060.30030.03750.4732-0.04440.15330.38850.07150.6262
59.16530.540.14788.91912.3042-0.967-0.5095-0.6743-0.35570.81790.3116-1.55550.7630.512-0.07860.4863-0.1870.03570.4733-0.17630.304
Refinement TLS groupSelection details: chain B and resid 93:103

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