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- PDB-4bq7: Crystal structure of the RGMB-Neo1 complex form 2 -

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Basic information

Entry
Database: PDB / ID: 4bq7
TitleCrystal structure of the RGMB-Neo1 complex form 2
Components
  • (RGM DOMAIN FAMILY MEMBER B) x 2
  • NEOGENIN
KeywordsCELL ADHESION
Function / homology
Function and homology information


trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / Netrin-1 signaling / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / intracellular vesicle ...trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / Netrin-1 signaling / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / intracellular vesicle / endoplasmic reticulum-Golgi intermediate compartment / protein secretion / negative regulation of protein secretion / BMP signaling pathway / coreceptor activity / side of membrane / postsynaptic density membrane / multicellular organismal-level iron ion homeostasis / signaling receptor activity / growth cone / intracellular iron ion homeostasis / cell adhesion / cadherin binding / membrane raft / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / glutamatergic synapse / cell surface / Golgi apparatus / signal transduction / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / Neogenin, C-terminal / Neogenin C-terminus / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / Neogenin, C-terminal / Neogenin C-terminus / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Neogenin / Repulsive guidance molecule B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.601 Å
AuthorsBell, C.H. / Healey, E. / van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
CitationJournal: Science / Year: 2013
Title: Structure of the Repulsive Guidance Molecule (Rgm)-Neogenin Signaling Hub
Authors: Bell, C.H. / Healey, E. / Van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
History
DepositionMay 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEOGENIN
B: NEOGENIN
C: RGM DOMAIN FAMILY MEMBER B
D: RGM DOMAIN FAMILY MEMBER B
E: RGM DOMAIN FAMILY MEMBER B
F: RGM DOMAIN FAMILY MEMBER B


Theoretical massNumber of molelcules
Total (without water)140,9726
Polymers140,9726
Non-polymers00
Water00
1
B: NEOGENIN
E: RGM DOMAIN FAMILY MEMBER B
F: RGM DOMAIN FAMILY MEMBER B


Theoretical massNumber of molelcules
Total (without water)70,4863
Polymers70,4863
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-23.6 kcal/mol
Surface area17440 Å2
MethodPISA
2
A: NEOGENIN
C: RGM DOMAIN FAMILY MEMBER B
D: RGM DOMAIN FAMILY MEMBER B


Theoretical massNumber of molelcules
Total (without water)70,4863
Polymers70,4863
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-23.7 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.690, 109.690, 187.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.914, -0.143, 0.3796), (-0.1626, -0.7283, -0.6657), (0.3717, -0.6702, 0.6424)-105.3, -20.31, 41.67
2given(-0.9232, -0.1378, 0.3588), (-0.1599, -0.7112, -0.6845), (0.3495, -0.6893, 0.6345)-105.4, -19.48, 40.25

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Components

#1: Protein NEOGENIN


Mass: 29221.842 Da / Num. of mol.: 2 / Fragment: FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P97798
#2: Protein RGM DOMAIN FAMILY MEMBER B / DRG11-RESPONSIVE AXONAL GUIDANCE AND OUTGROWTH OF NEURITE / DRAGON


Mass: 13318.698 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6NW40
#3: Protein RGM DOMAIN FAMILY MEMBER B / DRG11-RESPONSIVE AXONAL GUIDANCE AND OUTGROWTH OF NEURITE /


Mass: 27945.352 Da / Num. of mol.: 2 / Fragment: RESIDUES 169-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6NW40
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: 2.32 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL, PH 8.5, 0.2 M LITHIUM SULPHATE, 25 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 6.6→50 Å / Num. obs: 2508 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 121.5 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.5
Reflection shellResolution: 6.6→6.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.601→84.779 Å / SU ML: 0.99 / σ(F): 1.36 / Phase error: 27.17 / Stereochemistry target values: ML
Details: THERE IS AN AUTOCATALYTIC CLEAVAGE SITE PRESENT IN RGMB ( CHAINS C AND D), WHICH IS LOCATED BETWEEN RESIDUES ASP168 AND PRO169. IN ADDITION, NEO1 RESIDUES R967 AND R968 IN ( CHAIN A AND B) ...Details: THERE IS AN AUTOCATALYTIC CLEAVAGE SITE PRESENT IN RGMB ( CHAINS C AND D), WHICH IS LOCATED BETWEEN RESIDUES ASP168 AND PRO169. IN ADDITION, NEO1 RESIDUES R967 AND R968 IN ( CHAIN A AND B) WERE BUILT AS ALANINES.
RfactorNum. reflection% reflection
Rfree0.2799 230 9.2 %
Rwork0.2537 --
obs0.2561 2488 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.601→84.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 0 0 5714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175860
X-RAY DIFFRACTIONf_angle_d1.9347972
X-RAY DIFFRACTIONf_dihedral_angle_d15.7532126
X-RAY DIFFRACTIONf_chiral_restr0.132910
X-RAY DIFFRACTIONf_plane_restr0.0091008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.6013-8.31580.29271120.28391116X-RAY DIFFRACTION98
8.3158-84.78590.27311180.23651142X-RAY DIFFRACTION97
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)
1-2.2328-0.1047-3.974-0.45860.92372.276-0.0943-0.38521.0679-1.23250.34970.0138-0.16040.66410.01271.9630.0278-0.24782.25570.21682.1172-32.71874.9577-1.9249
23.18852.0437-4.86472.02792.39670.41040.29930.8024-0.41031.01290.13940.3895-0.51370.17301.57560.2398-0.45521.59130.08362.0927-59.2792-27.295310.8912
3-0.3154-2.02154.7356-0.3698-0.8058-0.56-0.18380.4475-0.2846-0.0641-0.01691.11360.103-0.99560.00612.17250.2836-0.04282.66580.27282.3359-86.77710.2457-17.3199
41.8480.8582-1.4322.643-1.82671.09-0.3289-0.06770.5234-0.12190.76610.1168-0.56330.428302.62340.10820.36931.54930.00012.13-52.181519.32932.3813
50.4262-0.20970.26633.99281.45857.4441-0.0336-0.32860.38590.28920.3566-0.0964-0.3150.6012-01.7104-0.0138-0.0441.64870.15831.8887-39.3858-23.673120.7424
6-4.2542-0.66853.45186.7632-3.52194.4544-0.22030.2084-0.25310.39-0.0481-0.0255-0.16920.471402.43190.23310.71551.652-0.11791.983-67.1247.328214.1933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 884:983)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 984:1088)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 884:983)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 984:1088)
5X-RAY DIFFRACTION5CHAIN C AND (RESID 138:321)
6X-RAY DIFFRACTION6CHAIN D AND (RESID 138:321)

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