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- PDB-3i84: The Crystal Structure of Human EMMPRIN N-terminal Domain 1 in P6(... -

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Basic information

Entry
Database: PDB / ID: 3i84
TitleThe Crystal Structure of Human EMMPRIN N-terminal Domain 1 in P6(1)22 space group
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 / neutrophil chemotaxis / embryo implantation / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / 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 / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Mar 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 1.3Oct 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1533
Polymers21,1172
Non-polymers351
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-27 kcal/mol
Surface area9140 Å2
MethodPISA
2
A: Cervical EMMPRIN
B: Cervical EMMPRIN
hetero molecules

A: Cervical EMMPRIN
B: Cervical EMMPRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3066
Polymers42,2354
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area8510 Å2
ΔGint-68 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.371, 100.371, 103.866
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-1-

CL

21B-115-

HOH

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Components

#1: Protein Cervical EMMPRIN


Mass: 10558.675 Da / Num. of mol.: 2 / Fragment: residues 13-103 / Mutation: A19D, N44D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCEP4 / Cell line (production host): HEK293 / Organ (production host): kidney / Production host: Homo Sapiens (human) / References: UniProt: Q54A51, UniProt: P35613*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 4.2 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2008
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→27.8 Å / Num. all: 21556 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.06 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1636 / Rsym value: 0.454 / % possible all: 94.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B5H

3b5h


Resolution: 2→27.765 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): -3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 987 4.97 %Random
Rwork0.1875 ---
all0.1885 19841 --
obs0.1885 19841 92.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.033 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 115.15 Å2 / Biso mean: 43.334 Å2 / Biso min: 18.85 Å2
Baniso -1Baniso -2Baniso -3
1--6.15 Å2-0 Å20 Å2
2---6.15 Å20 Å2
3---12.3 Å2
Refinement stepCycle: LAST / Resolution: 2→27.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 1 160 1423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131293
X-RAY DIFFRACTIONf_angle_d1.3541758
X-RAY DIFFRACTIONf_dihedral_angle_d18.426454
X-RAY DIFFRACTIONf_chiral_restr0.105204
X-RAY DIFFRACTIONf_plane_restr0.006222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.10560.21711350.19472621262192
2.1056-2.23740.23911510.18912664266494
2.2374-2.41010.23091420.20722716271695
2.4101-2.65240.22891430.20262711271195
2.6524-3.03590.21461400.17632778277896
3.0359-3.82330.16731480.15042736273693
3.8233-27.76730.20861280.19992628262884
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)
1refined4.01120.46941.75851.1649-0.4110.5783-0.02850.56010.1335-0.0545-0.06310.0610.0021-0.16570.10110.2244-0.0438-0.00710.3823-0.03190.218617.9754-34.6048-3.0256
23.5328-0.7373-0.97190.8783-0.81430.28820.24260.1837-0.4694-0.1711-0.17550.12740.4831-0.13210.250.23520.01590.0370.4105-0.05370.309
35.66172.5226-5.20056.8894-0.28475.9527-0.60370.2567-1.2859-0.5836-0.6557-0.54220.5917-0.76340.81210.3626-0.14220.10720.3813-0.03580.4525
43.8097-0.7301-1.45742.12621.07210.63350.02370.14510.23270.10420.0473-0.14120.04070.0539-0.05750.1916-0.00690.01190.28370.02040.195
58.4927-1.1636-2.87651.19060.8973.8485-0.14051.02821.3635-0.14170.4673-0.3490.2605-0.2539-0.13730.2586-0.0104-0.07690.52640.13170.3955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 22:92A22 - 92
2X-RAY DIFFRACTION2chain A and resid 93:103A93 - 103
3X-RAY DIFFRACTION3chain B and resid 13:18B13 - 18
4X-RAY DIFFRACTION4chain B and resid 24:92B24 - 92
5X-RAY DIFFRACTION5chain B and resid 93:103B93 - 103

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